From owner-chemistry@ccl.net Mon Oct 16 00:04:00 2006 From: "fuji fuji yamafuji6]-[yahoo.com" To: CCL Subject: CCL: DNA-Protein/Arginine guanidinium group interaction Message-Id: <-32804-061015235931-26938-pRtS2u7s8elpMK3MQi+36w:_:server.ccl.net> X-Original-From: "fuji fuji" Date: Sun, 15 Oct 2006 23:59:31 -0400 Sent to CCL by: "fuji fuji" [yamafuji6[]yahoo.com] Hello all, I would like to receive useful information and references (papers or books) on protein-DNA recognition, very particularly DNA-Arginine guanidinium moiety interaction. The all I know is, The majority of interactions involve O6 and/or N7 atoms of guanine bases forming hydrogen bonds with the charged ends of long flexible side chains from the basic residue arginine and 33% of the total of amino acid-base pair interactions are through ArgGuanine. Also recognitions through phosphate back bone (simple phosphate-guanidinium interactions or water mediated phosphate-guanidinium interactions) are possible (isn't it?). Now I need to know the following information : 1) During Arg-Guanine interaction is there any flanking nucleobases effect was observed? is this interaction favourable/strong when the flanking nucleobases are purine(s), particularly Guanine? is there any literature for this? 2) Also, is the phosphate-guanidinium (arginine) interactions favourable/strong with GC rich site? or is there any flanking nucleobase specificity observed for these kind of interactions? 3) If I want to analyse these things from the protein-DNA complex pdb files from protein data bank, how can I proceed? please guide me how to download pdf files and pdb codes also some useful softwares (freeware for academice purpose, either windows or linux platform) to analyse them. Looking forward for your useful information and references. Thanks in advance. Best Regards. From owner-chemistry@ccl.net Mon Oct 16 00:50:00 2006 From: "Soren Eustis soren---jhu.edu" To: CCL Subject: CCL:G: ECP Message-Id: <-32805-061016004821-21147-VesCxHpQXInPdP5bosEizg=server.ccl.net> X-Original-From: "Soren Eustis" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 15 Oct 2006 23:48:15 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren-x-jhu.edu] http://www.gaussian.com/g_ur/k_pseudo.htm Soren N. Eustis -----Original Message----- > From: owner-chemistry(0)ccl.net [mailto:owner-chemistry(0)ccl.net] Sent: Sunday, October 15, 2006 11:28 PM To: Eustis, Soren Subject: CCL:G: ECP Sent to CCL by: "Silviu Polosan" [Spol68*yahoo.com] Can anyone tell me how to introduce ECP (effective core potential) in Gaussian03? Thank youhttp://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 Mon Oct 16 01:25:00 2006 From: "Kalju Kahn kalju(_)chem.ucsb.edu" To: CCL Subject: CCL:G: Degrees of freedom: Thermochemistry Question Message-Id: <-32806-061015222217-28731-8bfiS8nOZVYQF0AvdkhSyA a server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sun, 15 Oct 2006 19:22:06 -0700 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju%a%chem.ucsb.edu] Dear Sarah, To calculate true vibrational enthalpies and entropies for a single conformer of a single covalent molecule in the gas phase, you need to plug the true vibrational frequencies into equations describing gas phase vibrational thermochemistry in harmonic approximation. Most intro stat mech and comp chem textbooks provide these, and they are also given on pg 7 of the Gaussian thermo white paper. I could send you an old Fortran 90 code that does this. To "subtract out" you will calculate the contribution from the modes you want to exclude using these formulas and subtract this contribution from the total. Your case is more difficult because your dimer has some (probably anharmonic) intermolecular vibrational modes in addition to internal rotations. The comparison with any experimental data is further complicated because there are likely several conformers; thus conformational entropy may be significant. What I am trying to say is that most likely there are several difficult-to-estimate corrections to thermochemistry in your system. Finally, is the gas phase thermochemistry what you really are interested in? The gas phase TD corrections may be quite irrelevant in solutions, especially if the solvent strongly affects the distribution of conformers and bond/angle vibration frequencies. Best regards, Kalju > I would like to obtain thermochemical data of the large alkyltin containing dimer I have optimized. The frequency calculation output details (see below) show "72 degrees of freedom that may cause significant error". I have been reading other CCL posts which suggest that these vibrations (which are internal rotations modes) can be corrected by Freq=hindrot and/or using the opt=tight keywords. The Gaussian White Paper on thermochemistry suggests "subtract out these values if you believe they are a source of error". If so, how do I subtract these out, for example in calculating the enthalpies, entropy and gibbs free energies of the molecule? > Any help and suggestions are greatly appreciated. I will post a summary of the feedback I receive. > > Thanking you in advance, > Sarah Whittleton > > ******************************** > Ph.D. Candidate > Department of Chemistry > Dalhousie University > Halifax, NS B3H 4J3 > Phone:(902) 494-7021 > ******************************** > > > > OU > > Principal axes and moments of inertia in atomic units: > 1 2 3 > EIGENVALUES -- ****************************** > X 0.99728 0.07372 0.00042 > Y -0.07370 0.99711 -0.01822 > Z -0.00176 0.01814 0.99983 > This molecule is an asymmetric top. > Rotational symmetry number 1. > Warning -- assumption of classical behavior for rotation > may cause significant error > Rotational temperatures (Kelvin) 0.00514 0.00499 0.00322 > Rotational constants (GHZ): 0.10704 0.10396 0.06707 > Zero-point vibrational energy 2025261.6 (Joules/Mol) > 484.04913 (Kcal/Mol) > Warning -- explicit consideration of 72 degrees of freedom as > vibrations may cause significant error> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Mon Oct 16 01:59:00 2006 From: "Dipankar Roy dipankarroy^^iitb.ac.in" To: CCL Subject: CCL:G: ECP Message-Id: <-32807-061016011558-6183-em5pTxP4vAx7vF19ejgd+A:+:server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 16 Oct 2006 10:39:13 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy]![iitb.ac.in] Hi, incorporating ECP=read in route section will do it. secify the Basis Set and ECP at the end of the geometry section for the atoms. For example #b3lyp/gen pseudo=read opt Test Job 0 1 X ........... X ............. X ............. X 0 lanl2dz **** X 0 lanl2dz Example of ECP incorporation is given in Gaussian Manual hope this will help -dipankar > Sent to CCL by: "Silviu Polosan" [Spol68*yahoo.com] > Can anyone tell me how to introduce ECP (effective core potential) in > Gaussian03? > > Thank you> > > > *********************************************** Dipankar Roy Graduate Student of Prof. R. B. Sunoj Computational Chemistry Laboratory Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) URL: http://www.geocities.com/dipankar_roy79/dipankar.html *********************************************** GETTING A SIMPLE ANSWER FROM A PROFESSOR IS LIKE GETTING A THIMBLE OF WATER FROM A FIRE HYDRANT. - PROF. LEN SHAPIRO, NDSU From owner-chemistry@ccl.net Mon Oct 16 02:54:01 2006 From: "Imran Predhanekar zmatrix||rediffmail.com" To: CCL Subject: CCL: how to Optimize Hydrated molecule Message-Id: <-32808-061016025112-20402-uUisTt9BVjBRr6nQmwBD1g|*|server.ccl.net> X-Original-From: "Imran Predhanekar" Date: Mon, 16 Oct 2006 02:51:11 -0400 Sent to CCL by: "Imran Predhanekar" [zmatrix%a%rediffmail.com] Dear sir, Some days back I asked this group how to optimize a hydrated molecule. In reply I was asked (by Dr Stewart) to send the molecular coordinates, which I did twice. I am again sending the coordinates (unhydrated for which I have to add 1 HCl and 5H2O). Please reply how it can be done starting with semiempirical level. regards imran 24 Molecule-1 0.000000 N -10.6851 0.3632 1.8250 C -9.8280 0.2478 0.6392 C -8.6239 1.2170 0.7285 C -7.7017 1.1491 -0.5243 C -6.4256 2.0624 -0.5134 C -6.7780 3.5752 -0.4040 N -5.5866 1.7159 0.6540 C -5.6581 1.8383 -1.7754 O -4.3910 1.3682 -1.7876 H -3.9332 1.2624 -2.6465 H -10.9886 1.3378 1.8885 H -10.1008 0.1791 2.6437 H -10.4302 0.4746 -0.2436 H -9.4768 -0.7841 0.5663 H -8.0471 0.9690 1.6226 H -9.0122 2.2315 0.8417 H -8.3105 1.4001 -1.3989 H -7.3783 0.1098 -0.6436 H -7.2338 3.8024 0.5610 H -5.8763 4.1866 -0.4934 H -7.4745 3.8721 -1.1916 H -5.3865 0.7141 0.6036 H -6.1411 1.8714 1.4978 O -6.2088 2.1027 -2.9819 Kind attn: Dr Stewart From owner-chemistry@ccl.net Mon Oct 16 09:24:01 2006 From: "Jens Carlsson jens||xray.bmc.uu.se" To: CCL Subject: CCL: solute conformations in water Message-Id: <-32809-061016052957-5581-XF4pxY5lL6qDWJ/X00zYDw*o*server.ccl.net> X-Original-From: "Jens Carlsson" Date: Mon, 16 Oct 2006 05:29:55 -0400 Sent to CCL by: "Jens Carlsson" [jens,xray.bmc.uu.se] I am looking for a (free) program that can predict low energy conformations of small organic molecules in water that are suitable as starting structures for MD simulations. Any suggestions? Best regards! / Jens Carlsson, Uppsala university (jens~~xray.bmc.uu.se) From owner-chemistry@ccl.net Mon Oct 16 09:59:01 2006 From: "wangyong,dicp.ac.cn" To: CCL Subject: CCL: How to calculate the energy consuming for electron transfer between two reagents? Message-Id: <-32810-061016042807-23959-9YT69KH90l2DUHdriLtbYQ:server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Mon, 16 Oct 2006 15:41:58 CST Sent to CCL by: [wangyong(-)dicp.ac.cn] Hello! all CCLers, I am now studying the mechanism of N-demethylation of substituted N,N-dimethylanilines mediated by cytochrome P450, where two mechanism were proposed: one is hydrogen atom transfer (HAT) occurring from C-H bond of amine to the Fe=O moiety of P450; and the other is first single electron transfer (SET) following by a proton shift from amine to P450. My question is how to calculate the energy consuming needed for the SET process, i.e., the energy needed for one electron transfer from N,N-dimethyaniline to Compound I of P450 (the Fe=O moiety)? Any response will be greatly appreciated! Yong Wang Theoretical and Computational Chemistry Center State Key Lab. of Molecular Reaction Dynamics Dalian Institute of Chemical Physics, the Chinese Academy of Sciences Dalian 116023, P. R. China ___________________________________ DICP WebMail, http://webmail.dicp.ac.cn From owner-chemistry@ccl.net Mon Oct 16 12:27:00 2006 From: "Rene Thomsen rt{}molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 2006 v1.6 Message-Id: <-32811-061016122516-30928-ZpeyRKOH5aCGNWmIKGZCDg%x%server.ccl.net> X-Original-From: "Rene Thomsen" Date: Mon, 16 Oct 2006 12:25:16 -0400 Sent to CCL by: "Rene Thomsen" [rt|-|molegro.com] Aarhus, Denmark, October 16th, 2006 - Molegro is pleased to announce a new release of Molegro Virtual Docker 2006, an integrated platform for predicting protein-ligand interactions available for Windows, Linux, and Mac OS X. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. New features in version 1.6: * Biomolecule Generator using transformation information from PDB files * Cropping Tool for removing non-relevant molecules and protein residues * Cavities found using the built-in cavity finder can now be stored in the workspace format (MVDML files) * New dialog for customizing the visual appearance (changing visualization schemes, light settings, and perspective projection) For more information, or to download a trial version, please visit our company website at: http://www.molegro.com or contact: Rene Thomsen, CEO Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus Denmark E-mail: rt{=}molegro.com Phone: (+45) 89423165 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Mon Oct 16 14:00:01 2006 From: "Vladimir G. Malkin vladimir.malkin^_^savba.sk" To: CCL Subject: CCL: visualization of spin-spin coupling pathways Message-Id: <-32812-061016134834-24078-KuhEjaYj32HnfSd5p9qGfQ=-=server.ccl.net> X-Original-From: "Vladimir G. Malkin" Date: Mon, 16 Oct 2006 13:48:34 -0400 Sent to CCL by: "Vladimir G. Malkin" [vladimir.malkin]|[savba.sk] Pertaining to a recent request on CCL, we would like to clarify the current situation about visualization of spin-spin coupling pathways (see the references below). Originally our approach has been implemented in our ReSpect code. However, as that part of the code is currently not distributed (currently we distribute free of the charge only the property block of the code: MAG), we do now make available the visualization in the older deMon code. The method uses double finite perturbation theory and writes the differential density (CDD) into a CUBE file which may be visualized by MOLEKEL (for example). We invite those, who are interested in the visualization, to contact us directly to obtain more detailed information on the distribution of the program. With the best wishes to the CCL community, Vladimir Malkin and Olga Malkina References. 1) O.L. Malkina, V.G. Malkin: Visualization of nuclear spin-spin coupling pathways by real-space functions Angewandte Chemie Int. Ed., 42, 4335-4338, 2003. 2) O.L. Malkina, "Interpretation of indirect nuclear spin-spin coupling constants",in "Calculation of NMR and EPR Parameters: Theory and Applications", Eds. M. Kaupp, M. Bhl, V.G. Malkin, Wiley, Weinheim, 2004. Dr. Vladimir G. Malkin, Dr.Sc. Institute of Inorganic Chemistry Slovak Academy of Sciences Dubravska cesta 9 vladimir.malkin^_^savba.sk SK-84536 Bratislava Fax (421-2) 5941-0444 Slovakia Phone (421-2) 5941-0469 From owner-chemistry@ccl.net Mon Oct 16 17:16:01 2006 From: "Jim Phillips jim::ks.uiuc.edu" To: CCL Subject: CCL: Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006 Message-Id: <-32813-061016171438-30290-cpWdPYH63L+A084ENr3Iow++server.ccl.net> X-Original-From: Jim Phillips Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 16 Oct 2006 16:14:33 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: Jim Phillips [jim * ks.uiuc.edu] http://www.ks.uiuc.edu/Training/Workshop/Cluster-2006.11/ In late November, the TCB Group will host a free workshop to teach users and system administrators how to specify, design, build, and run a high- performance Linux PC cluster for scientific computing. Starting with a discussion of clustering basics, participants will actually build their own cluster and get to test out their own applications. More details, including the scheduled program and copies of the lectures and texts of the hands-on tutorials, are available at the above web site. Applications must be received by November 6th; participants will be notified of their acceptance status by November 9th. - Tim Skirvin (tskirvin]~[ks.uiuc.edu) From owner-chemistry@ccl.net Mon Oct 16 20:48:01 2006 From: "Ben Vastine vastinator-.-gmail.com" To: CCL Subject: CCL:G: optimizations in gaussian break symmetry Message-Id: <-32814-061016125210-17567-6XIs3LqWxGf1ZimdIfkx+w-#-server.ccl.net> X-Original-From: "Ben Vastine" Content-Type: multipart/alternative; boundary="----=_Part_54217_32474097.1161011524714" Date: Mon, 16 Oct 2006 10:12:04 -0500 MIME-Version: 1.0 Sent to CCL by: "Ben Vastine" [vastinator===gmail.com] ------=_Part_54217_32474097.1161011524714 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline does anyone know how to avoid breaking the symmetry in optimizations in Gaussian? for example, here is the end of one my files: Leave Link 103 at Fri Oct 13 02:55:01 2006, MaxMem= 73400320 cpu: 10.1 (Enter /home/chem1/g03_dir/g03/l202.exe) Stoichiometry C34H53P2Rh Framework group C2[C2(RhH),X(C34H52P2)] Deg. of freedom 132 Full point group C2 NOp 2 Omega: Change in point group or standard orientation. Old FWG=C02 [C2(H1Rh1),X(C34H52P2)] New FWG=C02 [C2(Rh1H1),X(C34H52P2)] Error termination via Lnk1e in /home/chem1/g03_dir/g03/l202.exe at Fri Oct 13 02:55:03 2006. I've tried to change the grid, but I've had no success with that idea. What about step size? Thanks. ------=_Part_54217_32474097.1161011524714 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline does anyone know how to avoid breaking the symmetry in optimizations in Gaussian?  for example, here is the end of one my files:

Leave Link  103 at Fri Oct 13 02:55:01 2006, MaxMem=   73400320 cpu:      10.1
 (Enter /home/chem1/g03_dir/g03/l202.exe)
 Stoichiometry    C34H53P2Rh
 Framework group  C2[C2(RhH),X(C34H52P2)]
 Deg. of freedom   132
 Full point group                 C2      NOp   2
 Omega: Change in point group or standard orientation.

 Old FWG=C02  [C2(H1Rh1),X(C34H52P2)]
 New FWG=C02  [C2(Rh1H1),X(C34H52P2)]
 Error termination via Lnk1e in /home/chem1/g03_dir/g03/l202.exe at Fri Oct 13 02:55:03 2006.

I've tried to change the grid, but I've had no success with that idea.  What about step size?

Thanks.

------=_Part_54217_32474097.1161011524714--