From owner-chemistry@ccl.net Wed Jan 18 01:34:00 2006 From: "Pradipta Bandyopadhyay pradipta,,iitg.ernet.in" To: CCL Subject: CCL: Questions on the protonations of a HIV-1 protease (1aaq) Message-Id: <-30538-060118011950-456-gG2tyRiavE0YdQF3M/CbWw^_^server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 18 Jan 2006 11:34:18 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta_-_iitg.ernet.in] Protonation of catalytic ASPs is a tricky thing. For the free protease (without any lignad) people usually take both ASP as deprotonated (though I have seen papers where they have taken both as protonated). For the ligand bound forms of HIV-protease, people usually take one of the ASPs as protonated for peptide-based ligand (like SAQ, which is an actual drug). There are both computational and experimental works which support this (Biophysical Journal, 88, 867, 2005 for the computation and Biochemistry, 35, 9945, 1996 for the exp.) In our own work, we just kept one ASP protonated (Chemical Biology and Drug Design (in press)). However, it would be hard to generalize for all kind of ligands, I think. Pradipta > Sent to CCL by: Guosheng Wu [wu_guosheng2002[*]yahoo.com] > Dear listers, > > I am puzzled in assigning protonation states for some HIV-1 protease > complexes, and 1aaq(pdb code) > is a typical complex of many structures. > >> From this structure, one can see all of the 5 oxygen atoms (from Asp 25 >> & Asp 125, and ligand OH) > are very close to each other(2.7~3.1), and almost in the same plane. Also > each of the Gly 27 is > not far away(about 3.3 Angstrom) from the Asp 25, although the angle of > H-bond is not very good > (the Xray resolution is 2.5 Angstrom, exp. done in 1992; only one water is > given, but not close to > this part). > > Since the OO contact between Asp 25 and Asp 125 is 2.5 Angstrom, which is > about the distance of OO > in H5O2+ ion(2.4), one would like to assign a proton between them. > However, it seems very > difficulty to rationalize other polar interactions. > > One possible explanation may have something to do with quantum effect, > which may lead to some > modifications over the hybridization of the ligand Oxygen atom, as well as > some of the C-O-H bond > angles. Certainly, some kind of minimizations may be able to help on some > directions, but it > seems to me typical current force field would have trouble for this case. > > I wonder if you have done any study on this special complex, or similar > cases (actually many pdb > structures are like this one). I would really appreciate if you could > share some of your insights > with me. > > Best regards, > Guosheng > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com> > Job advertisements: http://www.ccl.net/jobs> > > Dr. Pradipta Bandyopadhyay Assistant Professor Dept. of Biotechnology Indian Institute of Technology, Guwahati Phone: 91-361-258-2213 (office) e-mail: pradipta],[iitg.ernet.in web: http://202.141.80.5/~pradipta/Pradipta.htm ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in From owner-chemistry@ccl.net Wed Jan 18 02:08:00 2006 From: "Dr. N. SUKUMAR nagams+*+rpi.edu" To: CCL Subject: CCL:G: Difference Between Two Different Types of Failure to Converge Message-Id: <-30539-060117235624-24045-uPSrglVASLnVtrhide2IKA+/-server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Tue, 17 Jan 2006 22:53:36 -0500 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams---rpi.edu] Convergence failure in link 502 is failure of SCF Convergence. See the page by David Young: http://ccl.osc.edu/cca/documents/dyoung/topics-framed/converge.shtml Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute ==============Original message text=============== On Tue, 17 Jan 2006 20:27:44 EST "Abrash, Samuel sabrash[-]richmond.edu" wrote: Sent to CCL by: "Abrash, Samuel" [sabrash(a)richmond.edu] Hi CCL Folks! I need some help understanding the difference between two different types of termination because of failure to converge. The first is the one I understand best. In this case, the optimization is set to run a maxiumum number of Berny cycles, and after the full number of allowed cycles (in my case 100), one or more of the four convergence criteria is unfulfilled. For this type of problem I have a pretty good idea of what to do. 1) Look at the output file to see if the structures are physically reasonable and moving toward convergence. 2a) If yes, just continue the job 2b) If no, try a different set of initial conditions, or modify the theory as needed. (Lots of options depending on the situation.) The second type of case is one where the failure to converge comes not on the final Berny cycle but on an early one. Here are the input file and the portion of the output file indicating the type of convergence failure for one of these jobs: Input: %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=12mw # UHF/3-21G OPT=(calcall, maxcycle=100) SCF=qc cyclopropanetrismethylene cation PBEPBE/aug-cc-pVDZ init geom arguslab low symm 1 2 C -0.317858 1.277419 0.119868 C -0.287771 2.616099 0.000000 C 0.643137 0.346751 0.202150 C 2.040557 0.274690 0.000000 C -0.694918 -0.054486 -0.097643 C -1.569659 -1.098761 0.000000 H 0.676927 3.142444 -0.048150 H -1.227851 3.185096 -0.049928 H 2.597937 1.169980 -0.312708 H 2.570431 -0.676665 0.155427 H -1.248715 -2.043628 0.462842 H -2.595146 -0.994986 -0.384198 --link1-- %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=12mw # UHF/6-31G Opt=(ReadFC, maxcycle=100) guess=read geom=allcheck scf=qc --link1-- %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=15mw # UPBEPBE/aug-cc-pVDZ Opt=(ReadFC, maxcycle=100) guess=read geom=allcheck --link1-- %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=15mw # UPBEPBE/aug-cc-pVDZ Opt=(rcfc, maxcycle=100) geom=allcheck --link1-- %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=15mw # UPBEPBE/aug-cc-pVDZ Freq guess=read geom=allcheck The job runs successfully for the two UHF jobs. Then on the second Berny cycle of the UPBEPBE/aug-cc-pVDZ there is a failure to converge. The full output for the second cycle is: GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Internal Forces: Max 0.004030705 RMS 0.001018805 Search for a local minimum. Step number 2 out of a maximum of 100 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using D2CorX and points 1 2 Trust test= 9.84D-01 RLast= 1.76D-01 DXMaxT set to 4.24D-01 Eigenvalues --- 0.00363 0.00457 0.00637 0.00716 0.00970 Eigenvalues --- 0.01542 0.03555 0.03561 0.03740 0.08693 Eigenvalues --- 0.09833 0.09905 0.11931 0.11966 0.12082 Eigenvalues --- 0.15236 0.15836 0.16085 0.33837 0.33897 Eigenvalues --- 0.37796 0.40451 0.40476 0.40507 0.40534 Eigenvalues --- 0.40557 0.42351 0.42412 0.47209 0.49435 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.00001000.00000 Eigenvalues --- 1000.000001000.00000 RFO step: Lambda=-9.49095729D-05. Quartic linear search produced a step of 0.03710. Iteration 1 RMS(Cart)= 0.00420970 RMS(Int)= 0.00000257 Iteration 2 RMS(Cart)= 0.00000342 RMS(Int)= 0.00000178 Iteration 3 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000178 Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) R1 2.63333 0.00137 -0.00069 0.00371 0.00302 2.63635 R2 2.65714 0.00191 0.00154 0.00325 0.00479 2.66192 R3 2.72881 0.00062 0.00278 -0.00162 0.00116 2.72997 R4 2.07080 0.00174 0.00171 0.00319 0.00491 2.07571 R5 2.07026 0.00186 0.00172 0.00341 0.00513 2.07539 R6 2.63334 0.00137 -0.00069 0.00370 0.00301 2.63635 R7 2.72882 0.00062 0.00278 -0.00163 0.00116 2.72997 R8 2.07080 0.00174 0.00171 0.00319 0.00491 2.07571 R9 2.07026 0.00186 0.00172 0.00341 0.00513 2.07539 R10 2.55046 0.00403 -0.00217 0.01109 0.00891 2.55937 R11 2.06913 0.00170 0.00168 0.00298 0.00466 2.07379 R12 2.06913 0.00170 0.00168 0.00298 0.00466 2.07379 A1 2.56260 0.00008 -0.00069 0.00018 -0.00051 2.56210 A2 2.65828 0.00019 0.00043 0.00084 0.00127 2.65956 A3 2.10190 -0.00016 0.00002 -0.00138 -0.00136 2.10054 A4 2.10755 0.00022 0.00019 0.00124 0.00143 2.10897 A5 2.07374 -0.00006 -0.00021 0.00014 -0.00007 2.07367 A6 2.56260 0.00008 -0.00069 0.00018 -0.00050 2.56210 A7 2.65829 0.00019 0.00043 0.00083 0.00127 2.65956 A8 2.10189 -0.00016 0.00002 -0.00138 -0.00136 2.10054 A9 2.10755 0.00022 0.00019 0.00124 0.00143 2.10898 A10 2.07374 -0.00006 -0.00021 0.00014 -0.00007 2.07367 A11 2.63309 -0.00027 0.00025 -0.00101 -0.00077 2.63233 A12 2.63309 -0.00027 0.00025 -0.00102 -0.00077 2.63233 A13 2.10983 0.00000 0.00017 -0.00111 -0.00094 2.10889 A14 2.10983 0.00000 0.00017 -0.00111 -0.00094 2.10889 A15 2.06352 0.00001 -0.00034 0.00223 0.00189 2.06541 D1 0.00000 0.00000 0.00000 0.00001 0.00001 0.00001 D2 3.14159 0.00000 0.00000 0.00001 0.00001 -3.14159 D3 -3.14158 0.00000 0.00000 0.00001 0.00001 -3.14157 D4 0.00001 0.00000 0.00000 0.00001 0.00001 0.00002 D5 0.00001 0.00000 0.00000 0.00000 0.00000 0.00001 D6 -0.00001 0.00000 0.00000 0.00000 0.00000 -0.00001 D7 0.00000 0.00000 0.00000 0.00001 0.00001 0.00001 D8 -3.14159 0.00000 0.00000 0.00000 0.00000 -3.14158 D9 -3.14159 0.00000 0.00000 0.00001 0.00001 -3.14158 D10 0.00001 0.00000 0.00000 0.00001 0.00001 0.00002 D11 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 D12 3.14158 0.00000 0.00000 0.00002 0.00002 -3.14159 D13 -0.00002 0.00000 0.00000 0.00002 0.00002 0.00001 D14 -0.00002 0.00000 0.00000 0.00002 0.00002 0.00000 D15 3.14158 0.00000 0.00000 0.00002 0.00002 3.14159 Item Value Threshold Converged? Maximum Force 0.004031 0.000450 NO RMS Force 0.001019 0.000300 NO Maximum Displacement 0.010397 0.001800 NO RMS Displacement 0.004210 0.001200 NO Predicted change in Energy=-5.395842D-05 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 -0.237228 0.763057 -0.028393 2 6 0 -0.534705 2.125159 -0.078167 3 6 0 0.767704 -0.223151 0.013368 4 6 0 2.135799 -0.495591 0.032816 5 6 0 -0.618580 -0.629581 0.017521 6 6 0 -1.567594 -1.595472 0.044403 7 1 0 0.272986 2.869305 -0.098334 8 1 0 -1.576033 2.473585 -0.097891 9 1 0 2.865548 0.325046 0.009436 10 1 0 2.503343 -1.529786 0.071622 11 1 0 -1.289422 -2.656312 0.083505 12 1 0 -2.633950 -1.336829 0.027627 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 C 0.000000 2 C 1.395096 0.00000 0 1.148793 -1.871634 0.000001 5 6 0 -0.876500 -0.000009 -0.000001 6 6 0 -2.230861 -0.000022 0.000000 7 1 0 2.245813 1.817045 -0.000012 8 1 0 0.667953 2.859072 0.000009 9 1 0 2.245853 -1.816996 0.000015 10 1 0 0.668017 -2.859059 -0.000011 11 1 0 -2.793270 -0.942353 0.000002 12 1 0 -2.793287 0.942299 0.000000 --------------------------------------------------------------------- Rotational constants (GHZ): 4.1801422 3.8590844 2.0066012 Standard basis: Aug-CC-pVDZ (5D, 7F) There are 192 symmetry adapted basis functions of A symmetry. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 192 basis functions, 324 primitive gaussians, 204 cartesian basis functio ns 21 alpha electrons 20 beta electrons nuclear repulsion energy 186.6386459511 Hartrees. NAtoms= 12 NActive= 12 NUniq= 12 SFac= 1.00Dáf? NAtFMM= 60 Big=F One-electron integrals computed using PRISM. NBasis= 192 RedAO= T NBF= 192 NBsUse= 192 1.00D-06 NBFU= 192 Initial guess read from the read-write file: Initial guess orbital symmetries: Alpha Orbitals: Occupied (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) Virtual (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) of initial guess= 0.8964 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. EnCoef did 4 forward-backward iterations EnCoef did 5 forward-backward iterations EnCoef did 2 forward-backward iterations EnCoef did 85 forward-backward iterations Rare condition: small coef for last iteration: -0.666D-15 EnCoef did 5 forward-backward iterations Rare condition: small coef for last iteration: 0.222D-15 EnCoef did 6 forward-backward iterations Rare condition: small coef for last iteration: 0.000Dáf? EnCoef did 7 forward-backward iterations Rare condition: small coef for last iteration: 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 1 Erem= -223.464925078448 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.432D-15 Matrix for removal 1 Erem= -225.612036927259 Crem= 0.000Dáf? EnCoef did 48 forward-backward iterations Matrix for removal 2 Erem= -230.056216034563 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.444D-15 Matrix for removal 1 Erem= -230.957780613922 Crem= 0.000Dáf? EnCoef did 48 forward-backward iterations Matrix for removal 3 Erem= -231.371944287973 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 6 Erem= -231.413745729862 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 1 Erem= -231.416133716719 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 13 Erem= -231.418900867161 Crem= 0.000Dáf? EnCoef did 59 forward-backward iterations Matrix for removal 18 Erem= -231.419070999074 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 11 Erem= -231.419112348980 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.419148641413 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.418778276146 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 9 Erem= -231.419169067006 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.554D-15 Matrix for removal 19 Erem= -231.418942288017 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 14 Erem= -231.419290263368 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419107556261 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 11 Erem= -231.420445394300 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419071776551 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 12 Erem= -231.420604168141 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419149178448 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 13 Erem= -231.420647898230 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.111D-14 Matrix for removal 19 Erem= -231.418949995443 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 17 Erem= -231.420648694361 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419096135031 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 9 Erem= -231.420657719207 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419104154891 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 14 Erem= -231.420671893769 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419081387961 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420658305176 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419145661317 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 17 Erem= -231.420673187415 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 19 Erem= -231.418960715007 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 16 Erem= -231.420675973150 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 19 Erem= -231.419021266252 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 16 Erem= -231.420681296646 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 19 Erem= -231.419335961191 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420587572061 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.440D-15 Matrix for removal 19 Erem= -231.418544675637 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 11 Erem= -231.420684293649 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419477236327 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420534345081 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.442D-15 Matrix for removal 19 Erem= -231.418796677540 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 10 Erem= -231.419651241752 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419280599829 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420608902185 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.221D-15 Matrix for removal 19 Erem= -231.418906193179 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420586795007 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419285531894 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 12 Erem= -231.420684711108 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.221D-15 Matrix for removal 19 Erem= -231.418892731624 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420585363376 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419289049853 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 14 Erem= -231.420702235767 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.331D-15 Matrix for removal 19 Erem= -231.418882803565 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420581194769 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419299060760 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 13 Erem= -231.420723664654 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.441D-15 Matrix for removal 19 Erem= -231.418855077350 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 12 Erem= -231.420727388183 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419324576409 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420570563941 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.110D-15 Matrix for removal 19 Erem= -231.418780647653 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 11 Erem= -231.420730549360 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419384341437 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420545387770 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.665D-15 Matrix for removal 19 Erem= -231.419018218195 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 18 Erem= -231.420693067494 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.444D-15 Matrix for removal 19 Erem= -231.419466794992 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420508813558 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.665D-15 Matrix for removal 19 Erem= -231.419030539317 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 18 Erem= -231.420688269172 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.777D-15 Matrix for removal 19 Erem= -231.419448841266 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420516657136 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.440D-15 Matrix for removal 19 Erem= -231.418503747344 Crem= 0.000Dáf? EnCoef did 15 forward-backward iterations Matrix for removal 13 Erem= -231.420736420738 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419515644416 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420488445027 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.220D-15 Matrix for removal 19 Erem= -231.418673619125 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 9 Erem= -231.420739298607 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.222D-15 Matrix for removal 18 Erem= -231.420515847041 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.419453081651 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.144D-14 Matrix for removal 19 Erem= -231.419131280349 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420653956973 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.222D-15 Matrix for removal 19 Erem= -231.419031179958 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 18 Erem= -231.420688123736 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.666D-15 Matrix for removal 18 Erem= -231.420517077761 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.419447848080 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.666D-15 Matrix for removal 19 Erem= -231.419123693065 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420655788332 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419006604895 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 12 Erem= -231.420741474519 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419483006932 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420501705978 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.221D-15 Matrix for removal 19 Erem= -231.418891457091 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420584815358 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419290379712 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 17 Erem= -231.420697653495 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.662D-15 Matrix for removal 19 Erem= -231.418878558166 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420579763623 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419302558715 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 17 Erem= -231.420741463049 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.418842382202 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 12 Erem= -231.420745177864 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.111D-14 Matrix for removal 19 Erem= -231.419335069289 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420566191137 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.220D-15 Matrix for removal 19 Erem= -231.418736422553 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 16 Erem= -231.420746777662 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 19 Erem= -231.419414870194 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420532350979 Crem= 0.000Dáf? >>>>>>>>>> Convergence criterion not met. SCF Done: E(UPBE-PBE) = -231.418804396 A.U. after 129 cycles Convg = 0.3553D-03 -V/T = 2.0061 S**2 = 0.7575 Annihilation of the first spin contaminant: S**2 before annihilation 0.7575, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/global/g03/l502.exe at Thu Dec 29 17:09:52 2005. Job cpu time: 0 days 4 hours 5 minutes 9.7 seconds. File lengths (MBytes): RWF= 51 Int= 0 D2E= 0 Chk= 7 Scr= 1 So I have two questions: 1) Is this a failure in geometric convergence, convergence of the integrals or what? I really don't understand WHAT it is that isn't converging. 2) What types of remedies are available when this occurs? If you saw this in one of your jobs what would you do next? Thanks, and once again I appreciate your help. Best, Samhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlJob advertisements: http://www.ccl.net/jobshttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Wed Jan 18 02:43:02 2006 From: "Satyan Sharma satyan]^[sun3.oulu.fi" To: CCL Subject: CCL:G: Freezing and ONIOM Message-Id: <-30540-060118020818-6368-g5ekSJORNpPB41zw5oZ2EA,+,server.ccl.net> X-Original-From: Satyan Sharma Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 18 Jan 2006 09:08:08 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Satyan Sharma [satyan!A!sun3.oulu.fi] Dear CCLers, I am using ONIOM to study enzyme action. I would like to freeze backbone atoms at their positions and the distance of a functional group from a donor and acceptor. From previous discussions in CCL and G03 manual its clear that I can use -1 option in the second field of Input to freeze atoms in the cartesian space but how to keep just the bond distances fixed. I tried using -1 option and at end of geometry(Cartesian) I specified X Y 2.0 F Y Z 2.0 F with opt=modredundant, I end up with error ONIOM: saving gridpoint 1 ONIOM: restoring gridpoint 3 ChrgS2: IScale= 0 0 5 5 5 5 Using ESP charges for embedding optimization. Need to have at least 3 QM atoms frozen Error termination via Lnk1e in /v/solaris9/appl/chem/gaussian/G03RevC.02/g03/l120.exe at Tue Jan 17 21:37:02 2006. Job cpu time: 0 days 0 hours 46 minutes 57.1 seconds. File lengths (MBytes): RWF= 116 Int= 0 D2E= 0 Chk= 19 Scr= 1 Segmentation Fault If I use F option to freeze all atoms and the bond I get the error Iteration 98 RMS(Cart)= 0.00002678 RMS(Int)= 4.18800938 Iteration 99 RMS(Cart)= 0.00002678 RMS(Int)= 4.18800939 Iteration100 RMS(Cart)= 0.00002678 RMS(Int)= 4.18800939 New curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in /v/solaris9/appl/chem/gaussian/G03RevC.02/g03/l101.exe at Wed Jan 18 08:48:44 2006. Job cpu time: 0 days 0 hours 0 minutes 8.4 seconds. File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 Scr= 1 Segmentation Fault ANy suggestions are welcome. Regards, Satyan Sharma From owner-chemistry@ccl.net Wed Jan 18 03:18:02 2006 From: "skpang!A!ctimail.com" To: CCL Subject: CCL: free software for curve fitting and mathematic manipulation of curves Message-Id: <-30541-060118024142-17723-ng9VmnZhIhN9GJtDQ2RyEg.:.server.ccl.net> X-Original-From: skpang]_[ctimail.com Date: Wed, 18 Jan 2006 15:41:29 +0800 (HKT) Sent to CCL by: skpang],[ctimail.com Dear all, Are there any free software like Origin for the curve-equation fitting? Also, which free software can carry out the mathematic manipulation of curves or plots (data points), such as intergrating and differentiatng of the curve/plot will give its integrated/differentiated shape? Regards, Patrick My e-mail address is: skpang*ctimail.com From owner-chemistry@ccl.net Wed Jan 18 06:45:00 2006 From: "Crous Werner wcrous]-[sun.ac.za wcrous]-[sun.ac.za" To: CCL Subject: CCL:G: Freezing and ONIOM Message-Id: <-30542-060118060456-31874-ffvouW64MN7TXm0qGrrflA__server.ccl.net> X-Original-From: "Crous Werner " Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 18 Jan 2006 12:26:18 +0200 MIME-Version: 1.0 Sent to CCL by: "Crous Werner [wcrous\a/sun.ac.za]" Hi there Use a value of less than -1 to freeze bonds in ONIOM. For example: X -2 (Cartesian coordinates) Y -2 A -3 B -3 This will freeze the X-Y bond and the A-B bond. Do not use modredundant when you are using microiterations for optimizations of the MM-system. Hope this helps Werner ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Werner Crous MSc. student Department of Chemistry and Polymer Science University of Stellenbosch Tel. +27 218083359 Cell. +27 824093822 Email:wcrous]^[sun.ac.za ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -----Original Message----- > From: owner-chemistry]^[ccl.net [mailto:owner-chemistry]^[ccl.net] Sent: 18 January 2006 10:07 To: Crous, Werner Subject: CCL:G: Freezing and ONIOM Sent to CCL by: Satyan Sharma [satyan!A!sun3.oulu.fi] Dear CCLers, I am using ONIOM to study enzyme action. I would like to freeze backbone atoms at their positions and the distance of a functional group from a donor and acceptor. From previous discussions in CCL and G03 manual its clear that I can use -1 option in the second field of Input to freeze atoms in the cartesian space but how to keep just the bond distances fixed. I tried using -1 option and at end of geometry(Cartesian) I specified X Y 2.0 F Y Z 2.0 F with opt=modredundant, I end up with error ONIOM: saving gridpoint 1 ONIOM: restoring gridpoint 3 ChrgS2: IScale= 0 0 5 5 5 5 Using ESP charges for embedding optimization. Need to have at least 3 QM atoms frozen Error termination via Lnk1e in /v/solaris9/appl/chem/gaussian/G03RevC.02/g03/l120.exe at Tue Jan 17 21:37:02 2006. Job cpu time: 0 days 0 hours 46 minutes 57.1 seconds. File lengths (MBytes): RWF= 116 Int= 0 D2E= 0 Chk= 19 Scr= 1 Segmentation Fault If I use F option to freeze all atoms and the bond I get the error Iteration 98 RMS(Cart)= 0.00002678 RMS(Int)= 4.18800938 Iteration 99 RMS(Cart)= 0.00002678 RMS(Int)= 4.18800939 Iteration100 RMS(Cart)= 0.00002678 RMS(Int)= 4.18800939 New curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in /v/solaris9/appl/chem/gaussian/G03RevC.02/g03/l101.exe at Wed Jan 18 08:48:44 2006. Job cpu time: 0 days 0 hours 0 minutes 8.4 seconds. File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 Scr= 1 Segmentation Fault ANy suggestions are welcome. Regards, Satyan Sharmahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Jan 18 08:52:00 2006 From: "Bruno Catalanotti brucatal _ unina.it" To: CCL Subject: CCL: biological application of quantum chemistry Message-Id: <-30543-060118070959-13907-EsNfr6an51/cN72tvjlIVA=-=server.ccl.net> X-Original-From: Bruno Catalanotti Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 18 Jan 2006 12:22:29 +0100 MIME-Version: 1.0 Sent to CCL by: Bruno Catalanotti [brucatal,unina.it] dear All, May anyone suggest me some reviews about biological application of ab-initio methods? I need fo teaching purposes. thank you Bruno Catalanotti -- Il messaggio e' stato analizzato alla ricerca di virus o contenuti pericolosi da MailScanner, ed e' risultato non infetto. From owner-chemistry@ccl.net Wed Jan 18 09:26:01 2006 From: "Noel O Boyle no228-x-cam.ac.uk" To: CCL Subject: CCL: free software for curve fitting and mathematic manipulation of curves Message-Id: <-30544-060118040736-10009-UBH7XGzTCl+f5jSnjyxM3Q^^^server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 18 Jan 2006 09:07:13 +0000 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228~!~cam.ac.uk] Grace http://plasma-gate.weizmann.ac.il/Grace/ On Wed, 2006-01-18 at 03:49 -0500, skpang!A!ctimail.com wrote: > Sent to CCL by: skpang],[ctimail.com > Dear all, > > Are there any free software like Origin for the curve-equation > fitting? Also, which free software can carry out the mathematic > manipulation of curves or plots (data points), such as intergrating and > differentiatng of the curve/plot will give its > integrated/differentiated shape? > > Regards, > > Patrick > > My e-mail address is: skpang++ctimail.com> > > From owner-chemistry@ccl.net Wed Jan 18 10:01:00 2006 From: "Lukasz Cwiklik lukasz.cwiklik%x%uochb.cas.cz" To: CCL Subject: CCL: free software for curve fitting and mathematic manipulation of curves Message-Id: <-30545-060118060826-32160-B6iIRa4vPvLxYAGv1Hxl9Q**server.ccl.net> X-Original-From: Lukasz Cwiklik Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 18 Jan 2006 12:08:20 +0100 MIME-Version: 1.0 Sent to CCL by: Lukasz Cwiklik [lukasz.cwiklik*o*uochb.cas.cz] On 1/18/06, skpang!A!ctimail.com wrote: > Sent to CCL by: skpang],[ctimail.com > Dear all, > > Are there any free software like Origin for the curve-equation > fitting? Dear Patrick, Curve-equation fitting can be done using Gnuplot. It is not as comfortable as in the GUI-based commertial software packages but works good and quickly. You can find a tutorial describing fitting data to user-defined functions here: http://t16web.lanl.gov/Kawano/gnuplot/intro/plotfunc-e.html Best regards, Lukasz Cwiklik -- Lukasz Cwiklik http://www.molecular.cz/~cwiklik From owner-chemistry@ccl.net Wed Jan 18 10:36:00 2006 From: "Goedele Roos groos%x%vub.ac.be" To: CCL Subject: CCL: biological application of quantum chemistry Message-Id: <-30546-060118092636-22008-8y1/taWEwLu+kXS5+pwLug^server.ccl.net> X-Original-From: Goedele Roos Date: Wed, 18 Jan 2006 15:26:28 +0100 (CET) Sent to CCL by: Goedele Roos [groos,,vub.ac.be] I don't have a review, but our group is very active on bio-applications! If you are intrested, I can sent some papers, Best regards, Goedele >Sent to CCL by: Bruno Catalanotti [brucatal,unina.it] >dear All, >May anyone suggest me some reviews about biological application of >ab-initio methods? I need fo teaching purposes. >thank you >Bruno Catalanotti > > >-- >Il messaggio e' stato analizzato alla ricerca di virus o >contenuti pericolosi da MailScanner, ed e' >risultato non infetto.> > > > Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Wed Jan 18 11:11:01 2006 From: "john furr john.furr~~gmail.com" To: CCL Subject: CCL:G: Dynamol 0.7 Release (Sorry if message repeat) Message-Id: <-30547-060118093455-1681-TNnFDgQi2k9KpBXwgExo1A^^server.ccl.net> X-Original-From: john furr Content-Type: multipart/alternative; boundary="----=_Part_5377_25287741.1137593312488" Date: Wed, 18 Jan 2006 09:08:32 -0500 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr]![gmail.com] ------=_Part_5377_25287741.1137593312488 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dynamol 0.7 is released free of charge to everyone. It is primarily a maintenance release. There is no associated license key or time limit restriction. Dynamol runs on Windows XP (maybe 2000) and modern Linux distributions. If the Fedora_Core_3 package will not install on your distro then send me the output of: { uname -a } and { gcc -v } and I will see about getting a working version to you. No promises. Enjoy! The only real new feature is Gaussian based molecular surfaces. The Dynamol Computational Engines have undergone a complete re-factorization. The result is a much faster and more stable piece of software. There are still some known bugs, but by and large you will find the platform to be stable. If it is not stable enough for you then please send me an error report at john.furr^^^gmail.com **Note: This is likely to be the last release of Dynamol with the current scripting language. The next version will replace the JScript language wit= h Python. Why Python? Good question. I had a personal liking for Ruby. However I think it is pretty fair to say that Python is fast becoming the language of chemistry. Open Eye, Schrodinger, Delano Scientific, and many other vendors are going this route. I think the comp chem community will agree that interoperability is good for everyone. I have had several conversations/emails with people who have been computational programmers much longer than I have. At their prodding I really started looking into Python. It is actually a wonderful language and integration with C++ is nice. I guess I have pretty much become a Python junky over the last couple of months. Thanks Joe. I have been learning the language from the inside out and I can say with certainty that Python is a very solid languag= e with excellent C++ extending and embedding capabilities. Ruby is still a great language, but alas it really is not as good a choice for computationa= l programming. But wait you say. What about Perl? **sigh** I have really tried to like Perl. Treated her like a little sister even. Perl is an overly expressive language. The syntax is almost as ugly (maybe more so) as the C++ syntax. If you are going to be uglier than C++ then at least be efficient!! Please note I am not really bashing Perl. I just think that Perl has seen it's time come and go. I literally learned the basics of Python with a couple of nights worth of reading. Sheesh I still don't know Perl well enough to figure out the code I wrote 2 years ago. My main point is that scientists will find Python a much easier language to learn than Perl. There are a couple of reasons for this. 1. The syntax is much simpler. Python embraces the one true way....while Perl believes all paths are great. To see what I mean foll= ow these instructions: 1. Fire up your python interpretor 2. import this 2. FORTRAN coders can still use a similar syntax to what they are used to. 3. The object oriented nature is very compatible with C++ and Java. So that is all well and good...but when will Dynamolship with Python? Well when it is ready is the best answer I can give you. Couple of months (2-4) probably. Anyway this was intended to be a product release and not the start of a flame war. I swear it! The website is in a complete state of disarray, but you should still be abl= e to find the Download link. One last thing: Anyone looking for a web hosting provider should steer very clear of StartLogic....you have been warned! Cheers John Furr Dynamol Inc. http://www.dynamol.com john.furr^^^gmail.com ------=_Part_5377_25287741.1137593312488 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dynamol 0.7 is released free of charge to everyone.  It is primarily a maintenance release.  There is no associated license key or time limit restriction.  Dynamol runs on Windows XP (maybe 20= 00) and modern Linux distributions.=20
If the Fedora_Core_3 package will not install on your distro then send me t= he output of:

{ <= /span>uname -a } and { gcc -v }

and I will see about getting a working version to you.  No promises. Enjoy!

The only real new feature is Gaussian based molecular surfaces.

The Dynamol Computational Engines have undergone a complete re-factorization. The result is a much faster and more stable piece of software.  There are still some known bugs, but by and large you will find the platform to be stable.  If it is not stable enough for you then please send me an error report a= t john.furr^^^gmail.com

**Note:  This is likely to be the last release of Dynamol with the current scripting language.  The next version will replace the JScript language with Python. 

Why Python?  Good question.  I had a personal liking for Ruby.  However I think it is pretty fair to say that Python is fast becoming the language of chemistry. Open Eye, Schrodinger, Delano Scientific, and many other vendors are going this route.  I think the comp chem community will agree that interoperability is good for everyone.  I have had several conversations/emails with people who have been computational programmers much longer than I have.  At their prodding I really started looking into Python.  It is actually a wonderful language and integration with C++ is nice.   I guess I have pretty much become a Python junky over the last couple of months.  Thanks Joe.  I have been learning the language from the inside out and I can say with certainty that Python is a very solid language with excellent C++ extending and embedding capabilities.  Ruby is still a great language, but alas it really is not as good a choice for computational programming.

But wait you say.  What about Perl? 
**sigh** 
I have really tried to like Perl.  Treated her like a little sister even.  Perl is an overly expressive language.  The syntax is almost as ugly (maybe more so) as the C++ syntax.  If you are going to be uglier than C++ then at least be efficient!!  Please note I am not really bashing Perl.  I just think that Perl has seen it's time come and go.  I literally learned the basics of Python with a couple of nights worth of reading.  Sheesh I still don't know Perl well enough to figure out the code I wrote 2 years ago.   My main point is that scientists will find Python a much easier language to learn than Perl.  There are a couple of reasons for this.
  1. The syntax is much simpler.   Python embraces the one true way....while Perl believes all paths are great.  To see what I mean follow these instructions:
    1. Fire up your python interpretor
    2. import this<= br>
  2. FORTRAN coders can still use a similar sy= ntax to what they are used to.
  3. The object oriented nature is very compatible with C++ and Java.=  

So that is all well and good...but when will Dynamol ship with Python?  Well when it is ready is the best= answer I can give you.  Couple of months (2-4) probably.

Anyway this was intended to be a product release and not the start of a fla= me war.  I swear it!

The website is in a complete state of disarray, but you should still be abl= e to find the Download link. =  

One last thing:  Anyone looking for  a web hosting provider should steer very clear of StartLogic....you have been warned!

Cheers

John Furr
Dynamol Inc.
http://www.dynamol.com
john.furr^^^gmail.com
 ------=_Part_5377_25287741.1137593312488-- From owner-chemistry@ccl.net Wed Jan 18 11:46:00 2006 From: "Tanja van Mourik t.vanmourik^ucl.ac.uk" To: CCL Subject: CCL: biological application of quantum chemistry Message-Id: <-30548-060118094015-5397-c6ALrj/CA4OxMQHqHT4q1A|-|server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 18 Jan 2006 14:39:29 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [t.vanmourik^_^ucl.ac.uk] Dear Bruno, > May anyone suggest me some reviews about biological application of > ab-initio methods? I need fo teaching purposes. Admittedly biased towards my own research, but there may be something of interest for you in the following article: First principles quantum chemistry in the life sciences T. van Mourik, Triennual Issue 'Chemistry and life science', Phil. Trans. Roy. Soc. Lond. A 362, 2653-2670 (2004). Best wishes, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik]_[ucl.ac.uk London WC1H 0AJ, UK home: tanja]_[van-mourik.me.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ================================================================= From owner-chemistry@ccl.net Wed Jan 18 12:21:01 2006 From: "Andreas Klamt klamt*o*cosmologic.de" To: CCL Subject: CCL: biological application of quantum chemistry Message-Id: <-30549-060118095519-17960-symDzLKxK28Vc1o5rFyrgA*server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 18 Jan 2006 15:54:50 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt*o*cosmologic.de] Dear Bruno, if you like you may consider our quantum chemically based prediction methods for - drug solubility - intestinal absorption - blood-brain partition coefficients - drug similarity as biological applications. For details see references under http://www.cosmologic.de/publications.html Andreas Bruno Catalanotti brucatal _ unina.it wrote: >Sent to CCL by: Bruno Catalanotti [brucatal,unina.it] >dear All, >May anyone suggest me some reviews about biological application of >ab-initio methods? I need fo teaching purposes. >thank you >Bruno Catalanotti > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt++cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Jan 18 12:56:00 2006 From: "Guosheng Wu wu_guosheng2002+/-yahoo.com" To: CCL Subject: CCL: Questions on the protonations of a HIV-1 protease (1aaq) Message-Id: <-30550-060118104606-1763-kkED8Vpic2zePE35rY/hUw~!~server.ccl.net> X-Original-From: Guosheng Wu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 18 Jan 2006 06:46:00 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Guosheng Wu [wu_guosheng2002%yahoo.com] Thanks a lot for your information. Obviously one should always look at the details of the special structure to make appropriate judgement, and that's why I put the specific pdb code in the title. The original paper put 4 H-bonds to the OH of the ligand in a figure based on distance contacts, and any kind of PMF scoring function would probably do the same thing, but one has to change some of the well-established concepts to tolerate this. I was trying to consult one experienced crystallographer on this case, but it turns out he was hoping modelling could help him out on this. By the way, many thanks to Dr. Elaine Meng for recommending a good QM/MM paper yesterday. It should be interesting to see how often our general chemistry intuition can get consistent results with high-level theories on the PKa prediction. Guosheng --- "Pradipta Bandyopadhyay pradipta,,iitg.ernet.in" wrote: > Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta_-_iitg.ernet.in] > Protonation of catalytic ASPs is a tricky thing. For the free protease > (without any lignad) people usually take both ASP as deprotonated (though > I have seen papers where they have taken both as protonated). > > For the ligand bound forms of HIV-protease, people usually take one of the > ASPs as protonated for peptide-based ligand (like SAQ, which is an actual > drug). There are both computational and experimental works which support > this (Biophysical Journal, 88, 867, 2005 for the computation > and > Biochemistry, 35, 9945, 1996 for the exp.) > > In our own work, we just kept one ASP protonated (Chemical Biology and > Drug Design (in press)). > > However, it would be hard to generalize for all kind of ligands, I think. > > Pradipta > > > > > Sent to CCL by: Guosheng Wu [wu_guosheng2002[*]yahoo.com] > > Dear listers, > > > > I am puzzled in assigning protonation states for some HIV-1 protease > > complexes, and 1aaq(pdb code) > > is a typical complex of many structures. > > > >> From this structure, one can see all of the 5 oxygen atoms (from Asp 25 > >> & Asp 125, and ligand OH) > > are very close to each other(2.7~3.1), and almost in the same plane. Also > > each of the Gly 27 is > > not far away(about 3.3 Angstrom) from the Asp 25, although the angle of > > H-bond is not very good > > (the Xray resolution is 2.5 Angstrom, exp. done in 1992; only one water is > > given, but not close to > > this part). > > > > Since the OO contact between Asp 25 and Asp 125 is 2.5 Angstrom, which is > > about the distance of OO > > in H5O2+ ion(2.4), one would like to assign a proton between them. > > However, it seems very > > difficulty to rationalize other polar interactions. > > > > One possible explanation may have something to do with quantum effect, > > which may lead to some > > modifications over the hybridization of the ligand Oxygen atom, as well as > > some of the C-O-H bond > > angles. Certainly, some kind of minimizations may be able to help on some > > directions, but it > > seems to me typical current force field would have trouble for this case. > > > > I wonder if you have done any study on this special complex, or similar > > cases (actually many pdb > > structures are like this one). I would really appreciate if you could > > share some of your insights > > with me. > > > > Best regards, > > Guosheng > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam protection around > > http://mail.yahoo.com> > > Job advertisements: http://www.ccl.net/jobs> > > > > > > > Dr. Pradipta Bandyopadhyay > Assistant Professor > Dept. of Biotechnology > Indian Institute of Technology, Guwahati > Phone: 91-361-258-2213 (office) > e-mail: pradipta-#-iitg.ernet.in > web: http://202.141.80.5/~pradipta/Pradipta.htm > > > ----------------------------------------------------------------------------------- > This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please > contact the sender by email and delete all copies; your cooperation in this regard is > appreciated. > http://www.iitg.ernet.in> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Wed Jan 18 13:31:00 2006 From: "Jason Gans jgans]=[lanl.gov" To: CCL Subject: CCL: free software for curve fitting and mathematic manipulation of curves Message-Id: <-30551-060118121607-10340-sUU5tcJaMlnVVoPY6b7vdQ..server.ccl.net> X-Original-From: Jason Gans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 18 Jan 2006 08:42:42 -0700 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Jason Gans [jgans .. lanl.gov] In addition to the excellent Grace program for *nix, there is PrestoPlot (windows only). http://www.mbg.cornell.edu/Shalloway_Lab_Presto.cfm Regards, Jason On Jan 18, 2006, at 1:54 AM, skpang!A!ctimail.com wrote: > Sent to CCL by: skpang],[ctimail.com > Dear all, > > Are there any free software like Origin for the curve-equation > fitting? Also, which free software can carry out the mathematic > manipulation of curves or plots (data points), such as intergrating and > differentiatng of the curve/plot will give its > integrated/differentiated shape? > > Regards, > > Patrick > > My e-mail address is: skpang++ctimail.com> To recover the email address of the author of the message, please > change> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > From owner-chemistry@ccl.net Wed Jan 18 14:06:01 2006 From: "john furr john.furr/a\gmail.com" To: CCL Subject: CCL:G: Dynamol 0.7 Release (Sorry if message repeat) Message-Id: <-30552-060118122717-22075-V/kjT8pyaXrhbNuXy66UEQ]|[server.ccl.net> X-Original-From: john furr Content-Type: multipart/alternative; boundary="----=_Part_7338_32735538.1137605231274" Date: Wed, 18 Jan 2006 12:27:11 -0500 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr,gmail.com] ------=_Part_7338_32735538.1137605231274 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Wow. Sorry about the formatting of that message! Not really sure what I did wrong? On 1/18/06, john furr john.furr~~gmail.com wrote: > > Sent to CCL by: john furr [john.furr]![gmail.com] > ------=3D_Part_5377_25287741.1137593312488 > Content-Type: text/plain; charset=3DISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > Dynamol 0.7 is released free of charge to > everyone. It is primarily a maintenance release. There is no associated > license key or time limit restriction. Dynamol > runs on Windows XP (maybe 2000) and modern > Linux distributions. > If the Fedora_Core_3 package will not install on your distro then send me > the output of: > > { uname -a } and { gcc -v } > > and I will see about getting a working version to you. No promises. > Enjoy! > > The only real new feature is Gaussian based molecular surfaces. > > The Dynamol Computational Engines have undergone a complete > re-factorization. The result is a much faster and more stable piece of > software. There are still some known bugs, but by and large you will fin= d > the platform to be stable. If it is not stable enough for you then pleas= e > send me an error report at john.furr]_[gmail.com > > **Note: This is likely to be the last release of Dynamol with the curren= t > scripting language. The next version will replace the JScript language > wit=3D > h > Python. > > Why Python? Good question. I had a personal liking for Ruby. However I > think it is pretty fair to say that Python is fast becoming the language > of > chemistry. Open Eye, Schrodinger, Delano Scientific, and many other > vendors > are going this route. I think the comp chem community will agree that > interoperability is good for everyone. I have had several > conversations/emails with people who have been computational programmers > much longer than I have. At their prodding I really started looking into > Python. It is actually a wonderful language and integration with C++ is > nice. I guess I have pretty much become a Python junky over the last > couple of months. Thanks Joe. I have been learning the language from th= e > inside out and I can say with certainty that Python is a very solid > languag=3D > e > with excellent C++ extending and embedding capabilities. Ruby is still a > great language, but alas it really is not as good a choice for > computationa=3D > l > programming. > > But wait you say. What about Perl? > **sigh** > I have really tried to like Perl. Treated her like a little sister even. > Perl is an overly expressive language. The syntax is almost as ugly > (maybe > more so) as the C++ syntax. If you are going to be uglier than C++ then > at > least be efficient!! Please note I am not really bashing Perl. I just > think that Perl has seen it's time come and go. I literally learned the > basics of Python with a couple of nights > worth > of reading. Sheesh I still don't know Perl well enough to figure out the > code I wrote 2 years ago. My main point is that scientists will find > Python a much easier language to learn than Perl. There are a couple of > reasons for this. > > 1. The syntax is much simpler. Python embraces the one true > way....while Perl believes all paths are great. To see what I mean > foll=3D > ow > these instructions: > 1. Fire up your python interpretor > 2. import this > 2. FORTRAN coders can still use a similar syntax to what they > are used to. > 3. The object oriented nature is very compatible with C++ and Java. > > > So that is all well and good...but when will > Dynamolship with Python? Well when it is > ready is the best answer I can give you. > Couple of months (2-4) probably. > > Anyway this was intended to be a product release and not the start of a > flame war. I swear it! > > The website is in a complete state of disarray, but you should still be > abl=3D > e > to find the Download link. > > One last thing: Anyone looking for a web hosting provider should steer > very clear of StartLogic....you have been warned! > > Cheers > > John Furr > Dynamol Inc. > http://www.dynamol.com > john.furr]_[gmail.com > > ------=3D_Part_5377_25287741.1137593312488 > Content-Type: text/html; charset=3DISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > top=3D > .js.OpenExtLink(window,event,this)">Dynamol 0.7 is released free of > charge to everyone.  It is primarily a maintenance release.  > There is no associated license key or time limit restriction.  href=3D > =3D3D"http://www.dynamol.com/" target=3D3D"_blank" onclick=3D3D"return > top.js.Ope=3D > nExtLink(window,event,this)">Dynamol runs on Windows XP (maybe > 20=3D > 00) and modern Linux distributions.=3D20 >
> > If the Fedora_Core_3 package will not install on your distro then send me > t=3D > he output of:
> >
> > { > <=3D > /span>uname -a } and { gcc -= v > span>}
> >
> > and I will see about getting a working version to you.  No > promises. r> > > Enjoy!
> >
> > The only real new feature is Gaussian based molecular surfaces.
> >
> > The Dynamol Computational Engines have undergone a complete > re-factorization. The result is a much faster and more stable piece of > software.  There are still some known bugs, but by and large you > will find the platform to be stable.  bold=3D > ;">If it is not stable enough for you then please send me an error report > a=3D > t onclick=3D3D"retur=3D > n top.js.OpenExtLink(window,event,this)"> > john.furr]_[gmail.com
> >
> > **Note:  This is likely to be the last release of Dynamol with the > current scripting language.  The next version will replace the > JScript language with Python. 
> >
> > Why Python?  Good question.  I had a personal liking for > Ruby.  However I think it is pretty fair to say that Python is > fast becoming the language of chemistry. Open Eye, Schrodinger, Delano > Scientific, and many other vendors are going this route.  I think > the comp chem community will agree that interoperability is good for > everyone.  I have had several conversations/emails with people who > have been computational programmers much longer than I have.  At > their prodding I really started looking into Python.  It is > actually a wonderful language and integration with C++ is > nice.   I guess I have pretty much become a Python junky over > the last couple of months.  Thanks Joe.  I have been learning > the language from the inside out and I can say with certainty that > Python is a very solid language with excellent C++ extending and > embedding capabilities.  Ruby is still a great language, but alas > it really is not as good a choice for computational programming. >
> >
> > But wait you say.  What about Perl? 
> > **sigh** 
> > I have really tried to like Perl.  Treated her like a little > sister even.  Perl is an overly expressive language.  The > syntax is almost as ugly (maybe more so) as the C++ syntax.  If > you are going to be uglier than C++ then at least be efficient!!  > Please note I am not really bashing Perl.  I just think that Perl > has seen it's time come and go.  I literally learned the basics of > =3D > top.js.OpenExtLink(window,event,this)">Python with a couple of nights > worth of reading.  Sheesh I still don't know Perl well enough to > figure out the code I wrote 2 years ago.   My main point is > that scientists will find Python a much easier language to learn than > Perl.  There are a couple of reasons for this.
> >
    >
  1. The syntax is much simpler.   Python embraces the one > true way....while Perl believes all paths are great.  To see what > I mean follow these instructions:
    >
    1. style=3D3D"font-styl=3D > e: italic;">Fire up your python interpretor
    2. sty=3D > le=3D3D"font-style: italic;">import > this<=3D > br> > >
  2. FORTRAN coders can still use a similar > sy=3D > ntax to what they are used to.
    >
  3. The object oriented nature is very compatible with C++ and > Java.=3D >  
    4. >
> >
> > So that is all well and good...but when will http://www.dynamol.=3D > com/" target=3D3D"_blank" onclick=3D3D"return top.js.OpenExtLink > (window,event,t=3D > his)">Dynamol ship with Python?  Well when it is ready is the > best=3D > answer I can give you.  Couple of months (2-4) probably. >
> >
> > Anyway this was intended to be a product release and not the start of a > fla=3D > me war.  I swear it!
> >
> > The website is in a complete state of disarray, but you should still be > abl=3D > e to find the onclick=3D > =3D3D"return top.js.OpenExtLink > (window,event,this)">Download link. =3D >  
> > >
> > One last thing:  Anyone looking for  a web hosting provider > should steer very clear of StartLogic....you have been warned!
> >
> > Cheers
> >
> > John Furr
> > Dynamol Inc.
> > top=3D > .js.OpenExtLink(window,event,this)">http://www.dynamol.com
> > onclick=3D3D"return =3D > top.js.OpenExtLink(window,event,this)">john.furr]_[gmail.com
> > > ------=3D_Part_5377_25287741.1137593312488-- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_7338_32735538.1137605231274 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Wow.  Sorry about the formatting of that message!
Not really sure what I did wrong? 

On 1/18/06, john furr john.furr~~gmail.= com <owner-chemistry_._ccl.= net > wrote:
Sent to CCL by: john furr [john.furr]![gmail.= com ]
------=3D_Part_5377_25287741.1137593312488
Content-Type: text/p= lain; charset=3DISO-8859-1
Content-Transfer-Encoding: quoted-printableContent-Disposition: inline

Dynamol < http://www.dynamol.com/>0.7 is released free of charge to
everyon= e.  It is primarily a maintenance release.  There is no= associated
license key or time limit restriction.  Dynamol< http://www.dynamol.com/>runs on Windows XP (maybe 2000) and modernLinux distributions.
If the Fedora_Core_3 package will not install on = your distro then send me
the output of:

{ uname -a } and { gcc -v= }

and I will see about getting a working version to you.  N= o promises.
Enjoy!

The only real new feature is Gaussian based mo= lecular surfaces.

The Dynamol Computational Engines have undergone a= complete
re-factorization. The result is a much faster and more stable piece of<= br>software.  There are still some known bugs, but by and large y= ou will find
the platform to be stable.  If it is not stable e= nough for you then please
send me an error report at john.furr]_[gma= il.com

**Note:  This is likely to be the last release = of Dynamol with the current
scripting language.  The next vers= ion will replace the JScript language wit=3D
h
Python.

Why Python?  Good question.  I = had a personal liking for Ruby.  However I
think it is pretty = fair to say that Python is fast becoming the language of
chemistry. Open= Eye, Schrodinger, Delano Scientific, and many other vendors
are going this route.  I think the comp chem community will a= gree that
interoperability is good for everyone.  I have had s= everal
conversations/emails with people who have been computational prog= rammers
much longer than I have.  At their prodding I really s= tarted looking into
Python.  It is actually a wonderful language and integration = with C++ is
nice.   I guess I have pretty much become a Python= junky over the last
couple of months.  Thanks Joe.  = ;I have been learning the language from the
inside out and I can say with certainty that Python is a very solid lan= guag=3D
e
with excellent C++ extending and embedding capabilities.&nb= sp; Ruby is still a
great language, but alas it really is not as go= od a choice for computationa=3D
l
programming.

But wait you say.  What about Perl?<= br>**sigh**
I have really tried to like Perl.  Treated her lik= e a little sister even.
Perl is an overly expressive language. &nbs= p;The syntax is almost as ugly (maybe
more so) as the C++ syntax.  If you are going to be uglier th= an C++ then at
least be efficient!!  Please note I am not real= ly bashing Perl.  I just
think that Perl has seen it's time co= me and go.  I literally learned the
basics of Python <http://dive= intopython.org/> with a couple of nights worth
of reading. &= nbsp;Sheesh I still don't know Perl well enough to figure out the
code I= wrote 2 years ago.   My main point is that scientists will find
Python a much easier language to learn than Perl.  There are = a couple of
reasons for this.

   1. The syntax is much = simpler.   Python embraces the one true
   way....wh= ile Perl believes all paths are great.  To see what I mean foll= =3D
ow
   these instructions:
   1. Fire up your = python interpretor
      2. import this      2. FORTRAN coders can still use a simi= lar syntax to what they
   are used to.
   3. The= object oriented nature is very compatible with C++ and Java.


So that is all well and good...but when will
Dynamol<http://www.dynamol.com/>ship with Py= thon?  Well when it is
ready is the best answer I can give you= .
Couple of months (2-4) probably.

Anyway this was intended to be a product release and not the start = of a
flame war.  I swear it!

The website is in a comple= te state of disarray, but you should still be abl=3D
e
to find the Do= wnload < http://www.dynamol.com/> link.
One last thing:  Anyone looking for  a web hostin= g provider should steer
very clear of StartLogic....you have been warned= !

Cheers

John Furr
Dynamol Inc.
http://= www.dynamol.com
john.furr]_[gmail.com<= /a>

------=3D_Part_5377_25287741.1137593312488
Content-Type: text= /html; charset=3DISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inl= ine

<a href=3D3D"http://= www.dynamol.com/" target=3D3D"_blank" onclick=3D3D"= return top=3D
.js.OpenExtLink(window,event,this)">Dynamol </a>0.7 is re= leased free of
charge to everyone.&nbsp; It is primarily a maintenan= ce release.&nbsp;
There is no associated license key or time limit r= estriction.&nbsp; <a href=3D
=3D3D"http://www.dynamol.com/<= /a>" target=3D3D"_blank" onclick=3D3D"return top.js.Ope= =3D
nExtLink(window,event,this)">Dynamol</a>  &n= bsp;    runs on Windows XP (maybe 20=3D
00) and modern Linux distributions.=3D20
<br>

If the Fe= dora_Core_3 package will not install on your distro then send me t=3D
he= output of:<br>

<br>

<span style=3D3D"fon= t-style: italic;"><span style=3D3D"font-style: italic;"= ;>{ <=3D
/span>uname -a</span> } and { <span style=3D3D"font-st= yle: italic;">gcc -v </=3D
span>}<br>

<br&= gt;

and I will see about getting a working version to you.&nbsp;= No promises.<b=3D
r>

Enjoy!<br>

<br>

The only real ne= w feature is Gaussian based molecular surfaces.<br>

<br>=

The Dynamol Computational Engines have undergone a complete
re-factorization. The result is a much faster and more stable piece of
s= oftware.&nbsp; There are still some known bugs, but by and large youwill find the platform to be stable.&nbsp; <span style=3D3D"fo= nt-weight: bold=3D
;">If it is not stable enough for you then please send me an er= ror report a=3D
t <a href=3D3D"mailto:john.furr]_[gmail.com" target= =3D3D"_blank" onclick=3D3D"retur=3D
n top.js.OpenExtLink(window,event,this)">
john.furr]_[gmail.com</a></span><br>
<br>

**Note:&nbsp; This is likely to be the last release= of Dynamol with the
current scripting language.&nbsp; The next version will replace the=
JScript language with Python.&nbsp; <br>

<br>
Why Python?&nbsp; Good question.&nbsp; I had a personal liking= for
Ruby.&nbsp; However I think it is pretty fair to say that Python is=
fast becoming the language of chemistry. Open Eye, Schrodinger, Delano<= br>Scientific, and many other vendors are going this route.&nbsp; I thi= nk
the comp chem community will agree that interoperability is good foreveryone.&nbsp; I have had several conversations/emails with people wh= o
have been computational programmers much longer than I have.&nbsp;= At
their prodding I really started looking into Python.&nbsp; It isactually a wonderful language and integration with C++ is
nice.&nbs= p;&nbsp; I guess I have pretty much become a Python junky over
the l= ast couple of months.&nbsp; Thanks Joe.&nbsp; I have been learning
the language from the inside out and I can say with certainty that
P= ython is a very solid language with excellent C++ extending and
embeddin= g capabilities.&nbsp; Ruby is still a great language, but alas
it re= ally is not as good a choice for computational programming.
<br>

<br>

But wait you say.&nbsp; What ab= out Perl?&nbsp; <br>

**sigh**&nbsp; <br>

= I have really tried to like Perl.&nbsp; Treated her like a little
sister even.&nbsp; Perl is an overly expressive language.&nbsp; The=
syntax is almost as ugly (maybe more so) as the C++ syntax.&nbsp; I= f
you are going to be uglier than C++ then at least be efficient!!&n= bsp;
Please note I am not really bashing Perl.&nbsp; I just think that P= erl
has seen it's time come and go.&nbsp; I literally learned the ba= sics of
<a href=3D3D"http= ://diveintopython.org/ " target=3D3D"_blank" onclick=3D3D"return =3D
to= p.js.OpenExtLink(window,event,this)">Python</a> with a couple= of nights
worth of reading.&nbsp; Sheesh I still don't know Perl we= ll enough to
figure out the code I wrote 2 years ago.&nbsp;&nbsp; My main po= int is
that scientists will find Python a much easier language to learn = than
Perl.&nbsp; There are a couple of reasons for this. <br>

<ol>
<li>The syntax is much simpler.&nbsp;&n= bsp; Python embraces the one
true way....while Perl believes all paths a= re great.&nbsp; To see what
I mean follow these instructions:<br&= gt;
  </li><ol><li><span style=3D3D"fon= t-style: italic;"><span style=3D3D"font-styl=3D
e: itali= c;">Fire up your python interpretor</span></span></l= i><li><span sty=3D
le=3D3D"font-style: italic;"><span style=3D3D"font= -style: italic;">import this<=3D
br>

  &n= bsp;   </span></span></li></ol><l= i>FORTRAN coders can still use a similar sy=3D
ntax to what they are used to.<br>
  </li><= li>The object oriented nature is very compatible with C++ and Java.=3D&nbsp;   </li>
</ol>

<br>
<= br>So that is all well and good...but when will <a href=3D3D" http://www.dynamol.=3D
com/"= target=3D3D"_blank" onclick=3D3D"return top.js.OpenExtLink(= window,event,t=3D
his)">Dynamol</a> ship with Python?&= nbsp; Well when it is ready is the best=3D
answer I can give you.&nbsp; Couple of months (2-4) probably.
&= lt;br>

<br>

Anyway this was intended to be a product= release and not the start of a fla=3D
me war.&nbsp; I swear it!<= br>

<br>

The website is in a complete state of disarray, b= ut you should still be abl=3D
e to find the <a href=3D3D"http://www.dynamol.com/" target=3D3D&= quot;_blank" onclick=3D
=3D3D"return top.js.OpenExtLink(window,event,this)">Downlo= ad</a>  link.&nbsp;=3D
&nbsp; <br>

=
<br>

One last thing:&nbsp; Anyone looking for&nbsp= ; a web hosting provider
should steer very clear of StartLogic....you have been warned! <br&g= t;

<br>

Cheers <br>

<br>

John= Furr<br>

Dynamol Inc.<br>

<a href=3D3D" http://www.dynamol.com/" targe= t=3D3D"_blank" onclick=3D3D"return top=3D
.js.OpenExtLink= (window,event,this)">http://www.= dynamol.com </a><br>
<span class=3D3D"sg">
<a = href=3D3D"mailto:john.furr]_[gmail.com" target=3D3D"_blank" onc= lick=3D3D"return =3D
top.js.OpenExtLink(window,event,this)">john.furr]_[gmail.com</a><br>
</span>
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------=_Part_7338_32735538.1137605231274-- From owner-chemistry@ccl.net Wed Jan 18 14:41:08 2006 From: "Shobe, David dshobe,,sud-chemieinc.com" To: CCL Subject: CCL:G: Difference Between Two Different Types of Failure to Converge Message-Id: <-30553-060118122127-19723-nM9HDi7z4eLaYBu6Rd7UMw : server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 18 Jan 2006 17:27:48 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe*o*sud-chemieinc.com] When you get the ">>>>>>>>>> Convergence criterion not met" message, this means that the solution to the SCF equations have not converged. Recall that SCF = self-consistend field: the equations are recalculated until the changes with each iteration are negligible: i.e. the equations are self-consistent. Gaussian puts by default a limit on the number of steps before it "gives up" and prints the error message. When the geometric convergence fails, one can continue the optimization using "geom=check", and you can increase the number of steps using "opt(maxcyc=###)". The analogous commands for SCF convergence failure are "guess=read" to continue the optimization where it left off, and "scf(maxcyc=###)" to increase the number of steps before Gaussian prints the error message. Unless you are doing a single point calculation, you should use "geom=check" with "guess=read", so that the geometry optimization will pick up at the point where it was interrupted by the SCF convergence failure. If SCF convergence repeatedly fails, you may want to try modifying the SCF algorithm. I usually try "scf=qc" or "scf(vshift=###)" with various values of "###". If those don't work there are a few others mentioned in the Gaussian manual and in the web site Dr. Sukumar recommended. Hope this helps, --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry..ccl.net [mailto:owner-chemistry..ccl.net] Sent: Wednesday, January 18, 2006 3:07 AM To: Shobe, David Subject: CCL:G: Difference Between Two Different Types of Failure to Converge Sent to CCL by: "Dr. N. SUKUMAR" [nagams---rpi.edu] Convergence failure in link 502 is failure of SCF Convergence. See the page by David Young: http://ccl.osc.edu/cca/documents/dyoung/topics-framed/converge.shtml Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute ==============Original message text=============== On Tue, 17 Jan 2006 20:27:44 EST "Abrash, Samuel sabrash[-]richmond.edu" wrote: Sent to CCL by: "Abrash, Samuel" [sabrash(a)richmond.edu] Hi CCL Folks! I need some help understanding the difference between two different types of termination because of failure to converge. The first is the one I understand best. In this case, the optimization is set to run a maxiumum number of Berny cycles, and after the full number of allowed cycles (in my case 100), one or more of the four convergence criteria is unfulfilled. For this type of problem I have a pretty good idea of what to do. 1) Look at the output file to see if the structures are physically reasonable and moving toward convergence. 2a) If yes, just continue the job 2b) If no, try a different set of initial conditions, or modify the theory as needed. (Lots of options depending on the situation.) The second type of case is one where the failure to converge comes not on the final Berny cycle but on an early one. Here are the input file and the portion of the output file indicating the type of convergence failure for one of these jobs: Input: %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=12mw # UHF/3-21G OPT=(calcall, maxcycle=100) SCF=qc cyclopropanetrismethylene cation PBEPBE/aug-cc-pVDZ init geom arguslab low symm 1 2 C -0.317858 1.277419 0.119868 C -0.287771 2.616099 0.000000 C 0.643137 0.346751 0.202150 C 2.040557 0.274690 0.000000 C -0.694918 -0.054486 -0.097643 C -1.569659 -1.098761 0.000000 H 0.676927 3.142444 -0.048150 H -1.227851 3.185096 -0.049928 H 2.597937 1.169980 -0.312708 H 2.570431 -0.676665 0.155427 H -1.248715 -2.043628 0.462842 H -2.595146 -0.994986 -0.384198 --link1-- %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=12mw # UHF/6-31G Opt=(ReadFC, maxcycle=100) guess=read geom=allcheck scf=qc --link1-- %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=15mw # UPBEPBE/aug-cc-pVDZ Opt=(ReadFC, maxcycle=100) guess=read geom=allcheck --link1-- %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=15mw # UPBEPBE/aug-cc-pVDZ Opt=(rcfc, maxcycle=100) geom=allcheck --link1-- %chk=/home/saabrash/C2H2TCalcs/cyclopropanetrismethylene+_1.chk %mem=15mw # UPBEPBE/aug-cc-pVDZ Freq guess=read geom=allcheck The job runs successfully for the two UHF jobs. Then on the second Berny cycle of the UPBEPBE/aug-cc-pVDZ there is a failure to converge. The full output for the second cycle is: GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Internal Forces: Max 0.004030705 RMS 0.001018805 Search for a local minimum. Step number 2 out of a maximum of 100 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using D2CorX and points 1 2 Trust test= 9.84D-01 RLast= 1.76D-01 DXMaxT set to 4.24D-01 Eigenvalues --- 0.00363 0.00457 0.00637 0.00716 0.00970 Eigenvalues --- 0.01542 0.03555 0.03561 0.03740 0.08693 Eigenvalues --- 0.09833 0.09905 0.11931 0.11966 0.12082 Eigenvalues --- 0.15236 0.15836 0.16085 0.33837 0.33897 Eigenvalues --- 0.37796 0.40451 0.40476 0.40507 0.40534 Eigenvalues --- 0.40557 0.42351 0.42412 0.47209 0.49435 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.00001000.00000 Eigenvalues --- 1000.000001000.00000 RFO step: Lambda=-9.49095729D-05. Quartic linear search produced a step of 0.03710. Iteration 1 RMS(Cart)= 0.00420970 RMS(Int)= 0.00000257 Iteration 2 RMS(Cart)= 0.00000342 RMS(Int)= 0.00000178 Iteration 3 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000178 Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) R1 2.63333 0.00137 -0.00069 0.00371 0.00302 2.63635 R2 2.65714 0.00191 0.00154 0.00325 0.00479 2.66192 R3 2.72881 0.00062 0.00278 -0.00162 0.00116 2.72997 R4 2.07080 0.00174 0.00171 0.00319 0.00491 2.07571 R5 2.07026 0.00186 0.00172 0.00341 0.00513 2.07539 R6 2.63334 0.00137 -0.00069 0.00370 0.00301 2.63635 R7 2.72882 0.00062 0.00278 -0.00163 0.00116 2.72997 R8 2.07080 0.00174 0.00171 0.00319 0.00491 2.07571 R9 2.07026 0.00186 0.00172 0.00341 0.00513 2.07539 R10 2.55046 0.00403 -0.00217 0.01109 0.00891 2.55937 R11 2.06913 0.00170 0.00168 0.00298 0.00466 2.07379 R12 2.06913 0.00170 0.00168 0.00298 0.00466 2.07379 A1 2.56260 0.00008 -0.00069 0.00018 -0.00051 2.56210 A2 2.65828 0.00019 0.00043 0.00084 0.00127 2.65956 A3 2.10190 -0.00016 0.00002 -0.00138 -0.00136 2.10054 A4 2.10755 0.00022 0.00019 0.00124 0.00143 2.10897 A5 2.07374 -0.00006 -0.00021 0.00014 -0.00007 2.07367 A6 2.56260 0.00008 -0.00069 0.00018 -0.00050 2.56210 A7 2.65829 0.00019 0.00043 0.00083 0.00127 2.65956 A8 2.10189 -0.00016 0.00002 -0.00138 -0.00136 2.10054 A9 2.10755 0.00022 0.00019 0.00124 0.00143 2.10898 A10 2.07374 -0.00006 -0.00021 0.00014 -0.00007 2.07367 A11 2.63309 -0.00027 0.00025 -0.00101 -0.00077 2.63233 A12 2.63309 -0.00027 0.00025 -0.00102 -0.00077 2.63233 A13 2.10983 0.00000 0.00017 -0.00111 -0.00094 2.10889 A14 2.10983 0.00000 0.00017 -0.00111 -0.00094 2.10889 A15 2.06352 0.00001 -0.00034 0.00223 0.00189 2.06541 D1 0.00000 0.00000 0.00000 0.00001 0.00001 0.00001 D2 3.14159 0.00000 0.00000 0.00001 0.00001 -3.14159 D3 -3.14158 0.00000 0.00000 0.00001 0.00001 -3.14157 D4 0.00001 0.00000 0.00000 0.00001 0.00001 0.00002 D5 0.00001 0.00000 0.00000 0.00000 0.00000 0.00001 D6 -0.00001 0.00000 0.00000 0.00000 0.00000 -0.00001 D7 0.00000 0.00000 0.00000 0.00001 0.00001 0.00001 D8 -3.14159 0.00000 0.00000 0.00000 0.00000 -3.14158 D9 -3.14159 0.00000 0.00000 0.00001 0.00001 -3.14158 D10 0.00001 0.00000 0.00000 0.00001 0.00001 0.00002 D11 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 D12 3.14158 0.00000 0.00000 0.00002 0.00002 -3.14159 D13 -0.00002 0.00000 0.00000 0.00002 0.00002 0.00001 D14 -0.00002 0.00000 0.00000 0.00002 0.00002 0.00000 D15 3.14158 0.00000 0.00000 0.00002 0.00002 3.14159 Item Value Threshold Converged? Maximum Force 0.004031 0.000450 NO RMS Force 0.001019 0.000300 NO Maximum Displacement 0.010397 0.001800 NO RMS Displacement 0.004210 0.001200 NO Predicted change in Energy=-5.395842D-05 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 -0.237228 0.763057 -0.028393 2 6 0 -0.534705 2.125159 -0.078167 3 6 0 0.767704 -0.223151 0.013368 4 6 0 2.135799 -0.495591 0.032816 5 6 0 -0.618580 -0.629581 0.017521 6 6 0 -1.567594 -1.595472 0.044403 7 1 0 0.272986 2.869305 -0.098334 8 1 0 -1.576033 2.473585 -0.097891 9 1 0 2.865548 0.325046 0.009436 10 1 0 2.503343 -1.529786 0.071622 11 1 0 -1.289422 -2.656312 0.083505 12 1 0 -2.633950 -1.336829 0.027627 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 C 0.000000 2 C 1.395096 0.00000 0 1.148793 -1.871634 0.000001 5 6 0 -0.876500 -0.000009 -0.000001 6 6 0 -2.230861 -0.000022 0.000000 7 1 0 2.245813 1.817045 -0.000012 8 1 0 0.667953 2.859072 0.000009 9 1 0 2.245853 -1.816996 0.000015 10 1 0 0.668017 -2.859059 -0.000011 11 1 0 -2.793270 -0.942353 0.000002 12 1 0 -2.793287 0.942299 0.000000 --------------------------------------------------------------------- Rotational constants (GHZ): 4.1801422 3.8590844 2.0066012 Standard basis: Aug-CC-pVDZ (5D, 7F) There are 192 symmetry adapted basis functions of A symmetry. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 192 basis functions, 324 primitive gaussians, 204 cartesian basis functio ns 21 alpha electrons 20 beta electrons nuclear repulsion energy 186.6386459511 Hartrees. NAtoms= 12 NActive= 12 NUniq= 12 SFac= 1.00Dáf? NAtFMM= 60 Big=F One-electron integrals computed using PRISM. NBasis= 192 RedAO= T NBF= 192 NBsUse= 192 1.00D-06 NBFU= 192 Initial guess read from the read-write file: Initial guess orbital symmetries: Alpha Orbitals: Occupied (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) Virtual (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) of initial guess= 0.8964 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. EnCoef did 4 forward-backward iterations EnCoef did 5 forward-backward iterations EnCoef did 2 forward-backward iterations EnCoef did 85 forward-backward iterations Rare condition: small coef for last iteration: -0.666D-15 EnCoef did 5 forward-backward iterations Rare condition: small coef for last iteration: 0.222D-15 EnCoef did 6 forward-backward iterations Rare condition: small coef for last iteration: 0.000Dáf? EnCoef did 7 forward-backward iterations Rare condition: small coef for last iteration: 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 1 Erem= -223.464925078448 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.432D-15 Matrix for removal 1 Erem= -225.612036927259 Crem= 0.000Dáf? EnCoef did 48 forward-backward iterations Matrix for removal 2 Erem= -230.056216034563 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.444D-15 Matrix for removal 1 Erem= -230.957780613922 Crem= 0.000Dáf? EnCoef did 48 forward-backward iterations Matrix for removal 3 Erem= -231.371944287973 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 6 Erem= -231.413745729862 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 1 Erem= -231.416133716719 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 13 Erem= -231.418900867161 Crem= 0.000Dáf? EnCoef did 59 forward-backward iterations Matrix for removal 18 Erem= -231.419070999074 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 11 Erem= -231.419112348980 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.419148641413 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.418778276146 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 9 Erem= -231.419169067006 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.554D-15 Matrix for removal 19 Erem= -231.418942288017 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 14 Erem= -231.419290263368 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419107556261 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 11 Erem= -231.420445394300 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419071776551 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 12 Erem= -231.420604168141 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419149178448 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 13 Erem= -231.420647898230 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.111D-14 Matrix for removal 19 Erem= -231.418949995443 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 17 Erem= -231.420648694361 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419096135031 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 9 Erem= -231.420657719207 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419104154891 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 14 Erem= -231.420671893769 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419081387961 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420658305176 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419145661317 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 17 Erem= -231.420673187415 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 19 Erem= -231.418960715007 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 16 Erem= -231.420675973150 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 19 Erem= -231.419021266252 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 16 Erem= -231.420681296646 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 19 Erem= -231.419335961191 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420587572061 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.440D-15 Matrix for removal 19 Erem= -231.418544675637 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 11 Erem= -231.420684293649 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419477236327 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420534345081 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.442D-15 Matrix for removal 19 Erem= -231.418796677540 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 10 Erem= -231.419651241752 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419280599829 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420608902185 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.221D-15 Matrix for removal 19 Erem= -231.418906193179 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420586795007 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419285531894 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 12 Erem= -231.420684711108 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.221D-15 Matrix for removal 19 Erem= -231.418892731624 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420585363376 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419289049853 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 14 Erem= -231.420702235767 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.331D-15 Matrix for removal 19 Erem= -231.418882803565 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420581194769 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419299060760 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 13 Erem= -231.420723664654 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.441D-15 Matrix for removal 19 Erem= -231.418855077350 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 12 Erem= -231.420727388183 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419324576409 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420570563941 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.110D-15 Matrix for removal 19 Erem= -231.418780647653 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 11 Erem= -231.420730549360 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419384341437 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420545387770 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.665D-15 Matrix for removal 19 Erem= -231.419018218195 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 18 Erem= -231.420693067494 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.444D-15 Matrix for removal 19 Erem= -231.419466794992 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420508813558 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.665D-15 Matrix for removal 19 Erem= -231.419030539317 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 18 Erem= -231.420688269172 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.777D-15 Matrix for removal 19 Erem= -231.419448841266 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420516657136 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.440D-15 Matrix for removal 19 Erem= -231.418503747344 Crem= 0.000Dáf? EnCoef did 15 forward-backward iterations Matrix for removal 13 Erem= -231.420736420738 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419515644416 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420488445027 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.220D-15 Matrix for removal 19 Erem= -231.418673619125 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 9 Erem= -231.420739298607 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.222D-15 Matrix for removal 18 Erem= -231.420515847041 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.419453081651 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.144D-14 Matrix for removal 19 Erem= -231.419131280349 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420653956973 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.222D-15 Matrix for removal 19 Erem= -231.419031179958 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 18 Erem= -231.420688123736 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.666D-15 Matrix for removal 18 Erem= -231.420517077761 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.419447848080 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.666D-15 Matrix for removal 19 Erem= -231.419123693065 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420655788332 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.111D-15 Matrix for removal 19 Erem= -231.419006604895 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 12 Erem= -231.420741474519 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419483006932 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420501705978 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.221D-15 Matrix for removal 19 Erem= -231.418891457091 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420584815358 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.222D-15 Matrix for removal 19 Erem= -231.419290379712 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 17 Erem= -231.420697653495 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.662D-15 Matrix for removal 19 Erem= -231.418878558166 Crem= 0.000Dáf? EnCoef did 6 forward-backward iterations Matrix for removal 19 Erem= -231.420579763623 Crem= 0.000Dáf? Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.419302558715 Crem= 0.000Dáf? Restarting incremental Fock formation. EnCoef did 100 forward-backward iterations Matrix for removal 17 Erem= -231.420741463049 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.000Dáf? Matrix for removal 19 Erem= -231.418842382202 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 12 Erem= -231.420745177864 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.111D-14 Matrix for removal 19 Erem= -231.419335069289 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420566191137 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: -0.220D-15 Matrix for removal 19 Erem= -231.418736422553 Crem= 0.000Dáf? EnCoef did 14 forward-backward iterations Matrix for removal 16 Erem= -231.420746777662 Crem= 0.000Dáf? Rare condition: small coef for last iteration: -0.444D-15 Matrix for removal 19 Erem= -231.419414870194 Crem= 0.000Dáf? EnCoef did 100 forward-backward iterations Matrix for removal 18 Erem= -231.420532350979 Crem= 0.000Dáf? >>>>>>>>>> Convergence criterion not met. SCF Done: E(UPBE-PBE) = -231.418804396 A.U. after 129 cycles Convg = 0.3553D-03 -V/T = 2.0061 S**2 = 0.7575 Annihilation of the first spin contaminant: S**2 before annihilation 0.7575, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/global/g03/l502.exe at Thu Dec 29 17:09:52 2005. Job cpu time: 0 days 4 hours 5 minutes 9.7 seconds. File lengths (MBytes): RWF= 51 Int= 0 D2E= 0 Chk= 7 Scr= 1 So I have two questions: 1) Is this a failure in geometric convergence, convergence of the integrals or what? I really don't understand WHAT it is that isn't converging. 2) What types of remedies are available when this occurs? If you saw this in one of your jobs what would you do next? Thanks, and once again I appreciate your help. Best, Samhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlJob advertisements: http://www.ccl.net/jobshttp://www.ccl.net/spammers.txt===========End of original message text===========http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed Jan 18 15:16:00 2006 From: "Ben Sattelle ben.sattelle() postgrad.manchester.ac.uk" To: CCL Subject: CCL: biological application of quantum chemistry Message-Id: <-30554-060118122743-22221-Y55HREWrxYkSmhVIuNz7Dg()server.ccl.net> X-Original-From: Ben Sattelle Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format="flowed" Date: Wed, 18 Jan 2006 16:37:03 +0000 MIME-Version: 1.0 Sent to CCL by: Ben Sattelle [ben.sattelle:+:postgrad.manchester.ac.uk] > May anyone suggest me some reviews about biological application of > ab-initio methods? I need fo teaching purposes. this book contains numerous examples & citations on this topic ... "Molecular Orbital Calculations for Biological Systems" , Ed. Anne-Marie Sapse. http://www.oup.co.uk/isbn/0-19-509873-0 ben. From owner-chemistry@ccl.net Wed Jan 18 17:01:00 2006 From: "christian.pilger__basf.com" To: CCL Subject: CCL: pi-stacking in ligand-protein interactions Message-Id: <-30557-060118125505-16471-ZHHJcmgC3+9rAcbpENCHvg%x%server.ccl.net> X-Original-From: christian.pilger##basf.com Content-type: text/plain; charset=US-ASCII Date: Wed, 18 Jan 2006 18:17:46 +0100 MIME-Version: 1.0 Sent to CCL by: christian.pilger{:}basf.com Dear CCLers, in one of my projects, I'm dealing with a protein that contains two phenylalanins oriented in such way that their phenylrings parallel each other. Between these two phenyl rings there is enough space to hold a ligand pi-system. My question: does it make a difference whether the ligand pi-system is electron rich (e.g. thiophen, pyrrole, indole etc.) or electron poor (pyridine, nitrobenzene etc.) ? Can a distinction be made, which type of pi-system would contribute more to ligand binding ? I can imagine, that in case the two phenylalanines were replaced by more electron rich tyrosines, an electron poor ligand pi-system could be advantegous because two electron rich system would repulse each other. Has anybody been concerned with this problem ? Are there references available in the literature that discuss this matter ? Any comments are welcome. Thanks in advance. Best regards, Christian _____________________________________________________________________________ BASF - Global Research Agricultural Products, GVA / FI E-Mail: christian.pilger a basf.com Postal Address: BASF Aktiengesellschaft, Ludwigshafen, D-67056, Ludwigshafen, Germany BASF - The Chemical Company BASF Aktiengesellschaft, Registered Office: 67056 Ludwigshafen, Germany Companies' Register: Amtsgericht Ludwigshafen, HRB 3000 Board of Executive Directors: Juergen Hambrecht, Chairman; Eggert Voscherau, Vice Chairman; Kurt W. Bock, John Feldmann, Andreas Kreimeyer, Klaus Peter Loebbe, Stefan Marcinowski, Peter Oakley Chairman of the Supervisory Board: Juergen Strube From owner-chemistry@ccl.net Wed Jan 18 16:26:00 2006 From: "Mgr. Lubos Vrbka lubos.vrbka]^[uochb.cas.cz" To: CCL Subject: CCL: Dynamol 0.7 Release (Sorry if message repeat) Message-Id: <-30556-060118145916-29290-QMI+zUiA/P/SfMUQD4Z+tw]=[server.ccl.net> X-Original-From: "Mgr. Lubos Vrbka" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Wed, 18 Jan 2006 20:59:31 +0100 MIME-Version: 1.0 Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka_+_uochb.cas.cz] john furr john.furr/agmail.com napsal(a): > Sent to CCL by: john furr [john.furr,gmail.com] > ------=_Part_7338_32735538.1137605231274 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > Wow. Sorry about the formatting of that message! > Not really sure what I did wrong? don't you have your mail account set up so that it sends the messages in html format? l. -- ..................................................... Mgr. Lubos Vrbka Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic http://www.molecular.cz/~vrbka ..................................................... From owner-chemistry@ccl.net Wed Jan 18 15:51:15 2006 From: "Roman D. Gorbunov gorbunov:_:theochem.uni-frankfurt.de" To: CCL Subject: CCL:G: Dipole moment with Gaussian. Message-Id: <-30555-060118132025-9407-iPNo7qewjlZK09cJDwuB+A_-_server.ccl.net> X-Original-From: "Roman D. Gorbunov" Sent to CCL by: "Roman D. Gorbunov" [gorbunov^theochem.uni-frankfurt.de] Dear All, I would like to calculate the dipole moment of a small molecule with Gaussian program. In my output files I can find the following lines: Dipole moment (Debye): X= 0.7722 Y= -3.9971 Z= 0.0078 Tot= 4.0710 It would seem that this is exactly what I need. However, a little bit further I can find the following lines: Test job not archived. ..... something ..... MSD=1.034e-09\RMSF=5.113e-05\Dipole=1.203046,-0.9454618,0.4733203\Dipo leDeriv=0.3104709,0.0526555,-0.0901773,0.0975203,0.3147646,-0.1101542, Where again one can see some "Dipole" which is not equal and even not proportional to the previously found value. Could anybody tell me what physical meaning have these two different vectors? Any reference where one can read about that will be also appreciated. Thank you in advance. From owner-chemistry@ccl.net Wed Jan 18 17:36:01 2006 From: "Chaitanya Krishna A icymist82,yahoo.com" To: CCL Subject: CCL: free software for curve fitting and mathematic manipulation of curves Message-Id: <-30558-060118130021-22509-5EyOrwSab3Xz7iijV9k+mw|-|server.ccl.net> X-Original-From: Chaitanya Krishna A Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1862628332-1137603614=:52124" Date: Wed, 18 Jan 2006 09:00:14 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Chaitanya Krishna A [icymist82-.-yahoo.com] --0-1862628332-1137603614=:52124 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, Even LabPlot does a good job. And it's more like Origin. http://labplot.sourceforge.net/ Regards, Chaitanya. SSCU. Indian Institute of Science. Bangalore, India. "Lukasz Cwiklik lukasz.cwiklik%x%uochb.cas.cz" wrote: Sent to CCL by: Lukasz Cwiklik [lukasz.cwiklik*o*uochb.cas.cz] On 1/18/06, skpang!A!ctimail.com wrote: > Sent to CCL by: skpang],[ctimail.com > Dear all, > > Are there any free software like Origin for the curve-equation > fitting? Dear Patrick, Curve-equation fitting can be done using Gnuplot. It is not as comfortable as in the GUI-based commertial software packages but works good and quickly. You can find a tutorial describing fitting data to user-defined functions here: http://t16web.lanl.gov/Kawano/gnuplot/intro/plotfunc-e.html Best regards, Lukasz Cwiklik -- Lukasz Cwiklik http://www.molecular.cz/~cwiklikhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Yahoo! Photos – Showcase holiday pictures in hardcover Photo Books. You design it and we’ll bind it! --0-1862628332-1137603614=:52124 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi,

Even LabPlot does a good job. And it's more like Origin.
http://labplot.sourceforge.net/

Regards,
Chaitanya.

SSCU.
Indian Institute of Science.
Bangalore, India.

"Lukasz Cwiklik lukasz.cwiklik%x%uochb.cas.cz" <owner-chemistry,,ccl.net> wrote:
Sent to CCL by: Lukasz Cwiklik [lukasz.cwiklik*o*uochb.cas.cz]
On 1/18/06, skpang!A!ctimail.com wrote:
> Sent to CCL by: skpang],[ctimail.com
> Dear all,
>
> Are there any free software like Origin for the curve-equation
> fitting?

Dear Patrick,
Curve-equation fitting can be done using Gnuplot. It is not as
comfortable as in the GUI-based commertial software packages but works
good and quickly.
You can find a tutorial describing fitting data to user-defined functions here:
http://t16web.lanl.gov/Kawano/gnuplot/intro/plotfunc-e.html

Best regards,
Lukasz Cwiklik


--
Lukasz Cwiklik
http://www.molecular.cz/~cwiklik






Yahoo! Photos – Showcase holiday pictures in hardcover
Photo Books. You design it and we’ll bind it! --0-1862628332-1137603614=:52124-- From owner-chemistry@ccl.net Wed Jan 18 18:11:00 2006 From: "Katrin Spiegel spiegel^^^vitae.cmm.upenn.edu" To: CCL Subject: CCL: biological application of quantum chemistry Message-Id: <-30559-060118124850-9679-VFPmwo7j3vq4oXMs2HPLpw%server.ccl.net> X-Original-From: Katrin Spiegel Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 18 Jan 2006 11:14:02 -0500 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Katrin Spiegel [spiegel-x-vitae.cmm.upenn.edu] Here are some references... "The role and perspective of ab initio molecular dynamics in the study of biological systems." Carloni P et al, Acc. Chem. Res. 35:455-64 (2002). "Applications of ab initio atomistic simulations to biology" Segall M. , J. Phys.: Condens. Matter, 14:2957 (2002) Cheers Katrin On Jan 18, 2006, at 9:08 AM, Bruno Catalanotti brucatal _ unina.it wrote: > Sent to CCL by: Bruno Catalanotti [brucatal,unina.it] > dear All, > May anyone suggest me some reviews about biological application of > ab-initio methods? I need fo teaching purposes. > thank you > Bruno Catalanotti > > > -- > Il messaggio e' stato analizzato alla ricerca di virus o > contenuti pericolosi da MailScanner, ed e' > risultato non infetto.> To recover the email address of the author of the message, please > change> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > From owner-chemistry@ccl.net Wed Jan 18 18:47:01 2006 From: "Leif Olson leif.olson_._kodak.com" To: CCL Subject: CCL: Simple molecular graphics...thanks Message-Id: <-30560-060118155208-17063-PXrrfL2C4yMTG672JOXAZA_+_server.ccl.net> X-Original-From: "Leif Olson" Sent to CCL by: "Leif Olson" [leif.olson]=[kodak.com] Hi CCL people, Thanks for the replies to my earlier post about simple molecular graphics. After submitting the post I ran across a website describing HFSmol, unfortunately not available yet but the author of this program (Steven Wheeler) apparently has a philosophy very similar to what I meant: http://www.ccc.uga.edu/~swheele2/hfsmol/index.php Interesting that Wheeler mentions Molecule for Macintosh as the kind of graphics he is aiming for...I have a copy of Molecule and I also think that output looks pretty good. But I don't know what format it is, it is a pain to transfer the images to my Windows PC, and I will probably have to junk my old Apple machine pretty soon anyway. So while I await HFSmol, there are several things that I thought worth a try: (1) xmakemol EPS output, as suggested by Mikael Johansson http://www.nongnu.org/xmakemol/ (2) Reconsider Ortep, maybe just using Toomas Tamm's recipe: http://www.kk.ttu.ee/toomas/research/ortep-for-qc.html (It would be nice if there was some similar info out there for Schakal, now available for free download: http://www.krist.uni-freiburg.de/ki/Mitarbeiter/Keller/schakal.html) (3) ChemCraft looks like it might do good simple graphics if needed, also looks good for orbitals and fancier color pictures (thanks to Denis Kondakov for this suggestion). http://www.chemcraftprog.com/description.html (4) A couple of people suggested Chem3D. It sounds promising. I'm not quite sure what the output looks like, but Cambridgesoft offers a trial download. Meanwhile some of the other programs that were suggested might very well have some buried functionality to make nice line-drawing molecular graphics. But that wasn't readily evident on websites or the online manuals, that focused on eye-catching full-color images of big molecules. Thanks again! Leif Olson Eastman Kodak Research Laboratories From owner-chemistry@ccl.net Wed Jan 18 19:22:00 2006 From: "T. Daniel Crawford crawdad..exchange.vt.edu" To: CCL Subject: CCL:G: Dipole moment with Gaussian. Message-Id: <-30561-060118183634-10801-DZuXyjDIq5ZRCSkF9O66hA%server.ccl.net> X-Original-From: "T. Daniel Crawford" Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Wed, 18 Jan 2006 17:49:24 -0500 Mime-version: 1.0 Sent to CCL by: "T. Daniel Crawford" [crawdad{:}exchange.vt.edu] Roman, The dipole moments given in the end-of-output summary are in atomic units (and presumably for a different orientation of your molecule). If you take the square-root of the sum of the squares of the components and multiply by 2.54175 Debye/au, you get 4.0710, which is the same as the total dipole moment you quote. -Daniel On 1/18/06 5:02 PM, "Roman D. Gorbunov gorbunov:_:theochem.uni-frankfurt.de" wrote: > Sent to CCL by: "Roman D. Gorbunov" [gorbunov^theochem.uni-frankfurt.de] > Dear All, > > I would like to calculate the dipole moment of a small molecule with Gaussian > program. In my output files I can find the following lines: > > Dipole moment (Debye): > X= 0.7722 Y= -3.9971 Z= 0.0078 Tot= 4.0710 > > It would seem that this is exactly what I need. However, a little bit further > I can find the following lines: > > Test job not archived. > .... something ..... > MSD=1.034e-09\RMSF=5.113e-05\Dipole=1.203046,-0.9454618,0.4733203\Dipo > leDeriv=0.3104709,0.0526555,-0.0901773,0.0975203,0.3147646,-0.1101542, > > Where again one can see some "Dipole" which is not equal and even not > proportional to the previously found value. > > Could anybody tell me what physical meaning have these two different vectors? > Any reference where one can read about that will be also appreciated. > > Thank you in advance.> > > -- T. Daniel Crawford Department of Chemistry crawdad[a]vt.edu Virginia Tech www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 540-231-3255 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt From owner-chemistry@ccl.net Wed Jan 18 19:56:00 2006 From: "Irida Kastrati ikastr2^uic.edu" To: CCL Subject: CCL: Program or Script to Calculate Atom-Atom Distances in pdb files Message-Id: <-30562-060118190335-25058-JrB0hFiQ1fzlkKD1xTTZGg()server.ccl.net> X-Original-From: "Irida Kastrati" Sent to CCL by: "Irida Kastrati" [ikastr2[a]uic.edu] Hello CCLers, Because of some excellent feedback I received when I asked for help about a year ago, I thought of using the CCL members expertise again this time. I am looking for a free program or script that can calculate all sulfur-sulfur distances in pdb files from the Protein Data Bank. The program or script should be able to read the massive database of protein structures from the Protein Data Bank, or a local copy of PDB files. Then, pinpoint S-S distances within a certain value, or calculate the actual distance. I have access to SYBYL. Any suggestion is very welcome! Thank you in advance for your time and help. Sincerely, Irida Kastrati e-mail: ikastr2###uic.edu University of IL at Chicago College of Pharmacy, Medicinal Chemistry From owner-chemistry@ccl.net Wed Jan 18 20:31:00 2006 From: "Lou Noodleman lou[]scripps.edu" To: CCL Subject: CCL: biological application of quantum chemistry Message-Id: <-30563-060118170311-32298-ipYRUcFzzc1/5tu6+5bAXA:+:server.ccl.net> X-Original-From: Lou Noodleman Date: Wed, 18 Jan 2006 13:27:42 -0800 (PST) Sent to CCL by: Lou Noodleman [lou##scripps.edu] To Bruno Catalanotti and CCL, For Biological Applications of DFT a number of relevant examples are discussed in our paper in Chem. Rev. 2004, 104, 459-508. Quantum Chemical Studies of Intermediates and Reaction Pathways in Selected Enzymes and Catalytic Synthetic Systems. Noodleman, L., Lovell, T., Han, W.-G., Li, J., Himo, F. along with many Ref's. The literature is very extensive, Lou Noodleman Molecular Biology, TPC15 The Scripps Research Institute La Jolla, CA92037 From owner-chemistry@ccl.net Wed Jan 18 21:06:01 2006 From: "john furr john.furr]=[gmail.com" To: CCL Subject: CCL: Dynamol 0.7 Release (Sorry if message repeat) Message-Id: <-30564-060118174054-1619-w54ZkMXt2qe0qJoD5Qe+qw||server.ccl.net> X-Original-From: john furr Content-Type: multipart/alternative; boundary="----=_Part_10135_18433453.1137624048158" Date: Wed, 18 Jan 2006 17:40:48 -0500 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr(a)gmail.com] ------=_Part_10135_18433453.1137624048158 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Good question? One message appears to have made it through ok. I was sending from a different account today as my previous email address expired. I wasn't expected both messages to go through. Anyway it certainly looked fine in gmail before I sent it. I do apologize. I gave myself a headache trying to decipher it. John On 1/18/06, Mgr. Lubos Vrbka lubos.vrbka]^[uochb.cas.cz < owner-chemistry-$-ccl.net> wrote: > > Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka_+_uochb.cas.cz] > john furr john.furr/agmail.com napsal(a): > > Sent to CCL by: john furr [john.furr,gmail.com] > > ------=3D_Part_7338_32735538.1137605231274 > > Content-Type: text/plain; charset=3DISO-8859-1 > > Content-Transfer-Encoding: quoted-printable > > Content-Disposition: inline > > > > Wow. Sorry about the formatting of that message! > > Not really sure what I did wrong? > don't you have your mail account set up so that it sends the messages in > html format? > > l. > > -- > .................................................... > Mgr. Lubos Vrbka > > Center for Biomolecules and Complex Molecular Systems > Institute of Organic Chemistry and Biochemistry > Academy of Sciences of the Czech Republic > Prague, Czech Republic > > http://www.molecular.cz/~vrbka > .................................................... > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_10135_18433453.1137624048158 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Good question?  One message appears to have made it through ok.  I was sending from a different account today as my previous email address expired.  I wasn't expected both messages to go through.  Anyway it certainly looked fine in gmail before I sent it.

I do apologize.  I gave myself a headache trying to decipher it.
John

On 1/18/06, Mgr. Lubos Vrbka lubos.vrbka]^[= uochb.cas.cz <owner-c= hemistry-$-ccl.net > wrote:
Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka_+_uochb.cas.= cz ]
john furr john.furr/agmail.com napsal(a):
> Sent to CCL by: john= furr [john.furr,gmail.com]
> ------= =3D_Part_7338_32735538.1137605231274
> Content-Type: text/plain; char= set=3DISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Dispos= ition: inline
>
> Wow.  Sorry about the formatting of= that message!
> Not really sure what I did wrong?
don't you have = your mail account set up so that it sends the messages in
html format?

l.

--
...................................= .................
Mgr. Lubos Vrbka

Center for Biomolecules and Co= mplex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
=
http://www.molecular.cz/~vrb= ka
....................................................



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------=_Part_10135_18433453.1137624048158-- From owner-chemistry@ccl.net Wed Jan 18 21:41:02 2006 From: "David J Anick david.anick%a%rcn.com" To: CCL Subject: CCL:G: Dipole moment with Gaussian. Message-Id: <-30565-060118173600-31490-MlhDo5MgI87aOVuibu+VxA##server.ccl.net> X-Original-From: "David J Anick" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 18 Jan 2006 16:56:52 -0500 MIME-Version: 1.0 Sent to CCL by: "David J Anick" [david.anick~!~rcn.com] Dear Roman, The archived data give the dipole moment in atomic units. The length of this vector is sqrt[(1.203..)^2+(-.945..)^2+(.473..)^2] = 1.60164 a.u. which is the same thing as 4.071 Debye. The orientation is probably that of the original molecule -- Gaussian re-orients your molecule to a "standard oreintation" before doing any calculations, and the Dip Moment in Debye refers to the standard orientation. David Anick PhD MD ----- Original Message ----- > From: "Roman D. Gorbunov gorbunov:_:theochem.uni-frankfurt.de" To: "Anick, David " Sent: Wednesday, January 18, 2006 4:08 PM Subject: CCL:G: Dipole moment with Gaussian. > Sent to CCL by: "Roman D. Gorbunov" [gorbunov^theochem.uni-frankfurt.de] > Dear All, > > I would like to calculate the dipole moment of a small molecule with Gaussian program. In my output files I can find the following lines: > > Dipole moment (Debye): > X= 0.7722 Y= -3.9971 Z= 0.0078 Tot= 4.0710 > > It would seem that this is exactly what I need. However, a little bit further I can find the following lines: > > Test job not archived. > .... something ..... > MSD=1.034e-09\RMSF=5.113e-05\Dipole=1.203046,-0.9454618,0.4733203\Dipo > leDeriv=0.3104709,0.0526555,-0.0901773,0.0975203,0.3147646,-0.1101542, > > Where again one can see some "Dipole" which is not equal and even not proportional to the previously found value. > > Could anybody tell me what physical meaning have these two different vectors? Any reference where one can read about that will be also appreciated. > > Thank you in advance.> > From owner-chemistry@ccl.net Wed Jan 18 22:16:00 2006 From: "Dr Seth Olsen s.olsen1{:}uq.edu.au" To: CCL Subject: CCL: Multiscale fluorescence simulation studies? Message-Id: <-30566-060118210226-7180-DMaBY7VuaJZ0VAMhiq/Tog]_[server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 19 Jan 2006 11:04:44 +1000 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1_-_uq.edu.au] Hi CCL'ers, I've been trying to chase up references that describe attempts to perform excited state dynamics on timescales relevant to fluorescence lifetimes. As someone with a background in ab initio excited state calculations and excited state dynamics simulations, I am quite aware that a straightforward excited state dynamics simulation on the nanoseconds to tens of nanoseconds timescale may be a bit of a challenge. What I'm interested in are questions of how the excited state potential surface changes the conformations sampled on the relevant timescale. I'm particularly interested in the case of a fluorophore bound to a protein. I've done some current contents searches, searches in relevant journals and googled it. I've found some items but it's not clear that its the sort of thing I'm looking for - namely a legitimate atomistic description of the stokes shift in a protein based (at the foundation) in first principles, that attempts to characterize timescales and possibly temperature dependencies of the stokes shift and the fluorescence spectral envelope. If anyone knows of any good references that they think may fit the bill, I'd be happy to receive them. Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1(0)uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms