From owner-chemistry@ccl.net Mon Nov 27 06:49:00 2006 From: "Patrick Pang skpang(!)ctimail.com" To: CCL Subject: CCL: possibility of change in molecular potential well depth Message-Id: <-33080-061127050109-31331-3NFRUlseiyP5otACz449wQ(0)server.ccl.net> X-Original-From: "Patrick Pang" Date: Mon, 27 Nov 2006 05:01:07 -0500 Sent to CCL by: "Patrick Pang" [skpang**ctimail.com] Dear all, For example, a Morse curve is used to describe the potential energy against distance of diatomic molecule. The potential well depth can be equal to the dissociation energy of diatomic molecule into two single atoms. Is it possible to change potential well depth? When the diatomic molecule is in excited state, the dissociation energy (potential well depth) becomes smaller. Does anyone konw how to increase the potential well depth? Theoretically, if the single atoms after dissociation are in excited state, the potential well depth will be increased. In reality, is it true? Is there any method for increasing the potential well depth? I think physcial chemists and physicists, particularly who are interested in molecular spectroscopy, chemical kinetics and molecules collision, can help me to answer these questions? My contact e-mail address is "skpang()ctimail.com". Thank you for your attention. Regards, Patrick From owner-chemistry@ccl.net Mon Nov 27 08:47:00 2006 From: "bo li libo7807-.-googlemail.com" To: CCL Subject: CCL:G: PBC calculation in G03 (bulk NaCl) Message-Id: <-33081-061127041634-27993-Rxiz1FCJZOEgmbCqW6mPKQ : server.ccl.net> X-Original-From: "bo li" Date: Mon, 27 Nov 2006 04:16:31 -0500 Sent to CCL by: "bo li" [libo7807%a%googlemail.com] Dear All, How about performance of Gaussian 03 (Revision C.02) Periodic Boundary Calculation (PBC) at Hartree-Fock level for 3D crystal for example NaCl. As I set kpoints equal 4, i found calculation can't go! I don't know something wrong with my input or anything else, I put my inputfile here. %chk=pbc.chk %mem=4GB %nproc=4 p hf/gen pbc=nkpoints=4 units=au iop(5/33=1) PBC 0 1 Na 0.00000000 0.00000000 0.00000000 Na 0.00000000 5.46000000 5.46000000 Na 5.46000000 0.00000000 5.46000000 Na 5.46000000 5.46000000 0.00000000 Cl 5.46000000 0.00000000 0.00000000 Cl 0.00000000 5.46000000 0.00000000 Cl 0.00000000 0.00000000 5.46000000 Cl 5.46000000 5.46000000 5.46000000 Tv 10.9200000 0.00000000 0.00000000 Tv 0.00000000 10.9200000 0.00000000 Tv 0.00000000 0.00000000 10.9200000 basis set : Phys. Rev. B 51, 3391 (1995) which is optimized for bulk NaCl. 120 basis functions, 352 primitive gaussians, and Currently job is for lattice constant = 5.78 A for HF ( J. Phys.: Condens. Matter. 1993, 5, 2969.) seems error in the output One-electron energy= 0.243171192747D+04 FoFJK: IHMeth= 1 ICntrl= 40 DoSepK=T KAlg= 1 I1Cent= 0 FoldK=F FoFCou: FMM=T IPFlag= 0 FMFlag= 990000 FMFlg1= 4097 NFxFlg= 0 DoJE=T BraDBF=F KetDBF=F FulRan=T. Symmetry not used in FoFCou. FMM levels: 3 Number of levels for PrismC: 1 PrismC: NFx=********** NFxT= 84 NFxU= 81. PrismC: NFx=********** NFxT= 84 NFxU= 81. PrismC: NFx=********** NFxT= 84 NFxU= 81. PrismC: NFx=********** NFxT= 84 NFxU= 81. PrismC: NFx=********** NFxT= 84 NFxU= 81. PrismC: NFx=********** NFxT= 84 NFxU= 81. PrismC: NFx=********** NFxT= 84 NFxU= 81. PrismC: NFx=********** NFxT= 84 NFxU= 81. 1/2 = -5327.275792634407 E= -2895.56386515975 why NFx=*************???? best wishes, Bo Li From owner-chemistry@ccl.net Mon Nov 27 09:49:01 2006 From: "Shobe, David David.Shobe!=!sud-chemie.com" To: CCL Subject: CCL: possibility of change in molecular potential well depth Message-Id: <-33082-061127092154-30585-9zUnCXGfQDLavvFBqBypyA()server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 Nov 2006 15:21:22 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe a sud-chemie.com] All you need to do to change the well depth is to multiply by a scalar. i.e. if M(r) is the Morse potential for molecule AB, then kM(r) is another Morse potential with a different well depth but the same equilibrium bond distance (r0). Changing r0 is a somewhat trickier, as M(kr) has not only a different r0 but also a different well depth from M(r). --David Shobe -----Original Message----- > From: owner-chemistry*_*ccl.net [mailto:owner-chemistry*_*ccl.net] Sent: Monday, November 27, 2006 7:11 AM To: Shobe, David Subject: CCL: possibility of change in molecular potential well depth Sent to CCL by: "Patrick Pang" [skpang**ctimail.com] Dear all, For example, a Morse curve is used to describe the potential energy against distance of diatomic molecule. The potential well depth can be equal to the dissociation energy of diatomic molecule into two single atoms. Is it possible to change potential well depth? When the diatomic molecule is in excited state, the dissociation energy (potential well depth) becomes smaller. Does anyone konw how to increase the potential well depth? Theoretically, if the single atoms after dissociation are in excited state, the potential well depth will be increased. In reality, is it true? Is there any method for increasing the potential well depth? I think physcial chemists and physicists, particularly who are interested in molecular spectroscopy, chemical kinetics and molecules collision, can help me to answer these questions? My contact e-mail address is "skpang . ctimail.com". Thank you for your attention. Regards, Patrickhttp://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 Mon Nov 27 11:01:00 2006 From: "Phil Hultin hultin_+_cc.umanitoba.ca" To: CCL Subject: CCL:G: Protonation and g03 Message-Id: <-33083-061127105122-22485-rsHEOiLM8Kroy5ID8Dt9Uw[a]server.ccl.net> X-Original-From: "Phil Hultin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 Nov 2006 09:51:10 -0600 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin(-)cc.umanitoba.ca] Re: protonation sites of diamines and other organic compounds I don't know about using ab initio methods to rationalize/predict protonation sites - obviously it is doable in principle but may be difficult to achieve in practice especially if you want condensed-phase (solvated) results. If you just want semi-quantitative results, try the SPARC online calculator > from the University of Georgia: http://ibmlc2.chem.uga.edu/sparc/ The SPARC algorithm has been documented in the peer-reviewed literature, and it has been validated against quite a range of structures and experimental results. You would not want to use it to understand very subtle effects but it appears to be quite reliable for most straightforward structure-activity relationships. Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin+*+cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin -----Original Message----- > From: owner-chemistry+*+ccl.net [mailto:owner-chemistry+*+ccl.net] Sent: November 27, 2006 1:30 AM To: Hultin, Philip G. Subject: CCL:G: Protonation and g03 Sent to CCL by: "fuji fuji" [yamafuji6]|[yahoo.com] dear all, My molecule have two protonation sites (say for example N2 and N5). But at pH=7 there is only one protonated form exists in addition with the unprotonated form (around 50:50). So, I would like to analyze the protonation site at pH=7. Is it possible to do it in g03? if so wat kind of calculations i can perform? Analytical frequency calculations with MP2/6-311+G(d) level gave me all real frequencies for N2 protonated form and two negative frequencies for N5 protonated form. Is this enough to proove that N2 protonation is favorable? (also, experimental results are in good agreement with this) Is it possible to include the pH effect in a g03 calculation? if so please give me the syntax/keyword. Looking forward for your reply. Thank you very much.http://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 Nov 27 11:36:00 2006 From: "Jens Spanget-Larsen spanget:_:ruc.dk" To: CCL Subject: CCL:G: Protonation and g03 Message-Id: <-33084-061127070808-9325-c7QS/mImtPmBxmPzNWNOgg*_*server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 27 Nov 2006 12:15:07 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget- -ruc.dk] Dear Fuji, with the options "density prop" the output contains electrostatic properties, including electric potentials (EPs) at the various centers in the molecule. The EP values tend to correlate nicely with the basicities of similar centers, for example, different aza-centers in aza-aromates: The more negative is EP, the more negative is pKa for protonation of the center in question. Good results may also be obtained with semiempirical approaches, such as the W parameter, see the following references. Yours, Jens >--< O. Dmitrenko, W. Reischl, R. D. Bach, J. Spanget-Larsen: "TD DFT Computational Insight into the Origin of Wavelength-Dependent E/Z Photoisomerization of Urocanic Acid", J. Phys. Chem. A 108, 5662-5669 (2004) E. Sikorska, H. Szymusiak, I. V. Khmelinskii, A. KozioĊ‚owa, J. Spanget-Larsen, M. Sikorski, "Spectroscopy and photophysics of alloxazines studied in their ground and first excited states", J. Photochem. Photobiol. A, 158, 45-53 (2003) J. Spanget-Larsen, "Structure-Reactivity Correlations for Aza-arenes. Proton Affinities, pKa Values, Hydrogen-Deuterium Exchange Rates, and Radical-Induced 13C Shifts", J. Phys. Org. Chem. 8, 496-505 (1995) J. Waluk, W. Rettig, J. Spanget-Larsen, "Ground and Excited-State Protonation of Aminoquinoxalines", J. Phys. Chem. 92, 6930-6935 (1988) J. Spanget-Larsen, "A Structure-Reactivity Relationship for the Basicity of Aza-arenes", J. Chem. Soc. Perkin Trans II, 417-419 (1985) ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget(a)ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ fuji fuji yamafuji6/ayahoo.com wrote: > Sent to CCL by: "fuji fuji" [yamafuji6]|[yahoo.com] > dear all, > My molecule have two protonation sites (say for example N2 and N5). Butat pH=7 there is only one protonated form exists in addition with the unprotonated form (around 50:50). So, I would like to analyze the protonation site at pH=7. Is it possible to do it in g03? if so wat kind of calculations i can perform? Analytical frequency calculations with MP2/6-311+G(d) level gave me all real frequencies for N2 protonated form and two negative frequencies for N5 protonated form. Is this enough to proove that N2 protonation is favorable? (also, experimental results are in good agreement with this) Is it possible to include the pH effect in a g03 calculation? if so please give me the syntax/keyword. Looking forward for yourreply. Thank you very much. From owner-chemistry@ccl.net Mon Nov 27 12:11:01 2006 From: "Damjan Krstajic Damjan.Krstajic~!~discoverybus.com" To: CCL Subject: CCL: myStructure - opensource database app Message-Id: <-33085-061127102747-7553-6lv08iB4xBHOXr6e1xueBw#server.ccl.net> X-Original-From: "Damjan Krstajic" Date: Mon, 27 Nov 2006 10:27:45 -0500 Sent to CCL by: "Damjan Krstajic" [Damjan.Krstajic!A!discoverybus.com] Dear All, My name is Damjan Krstajic and I am founder of an opensource project myStructure http://sourceforge.net/projects/mystructure myStructure is intended for QSAR specialists and is currently used at the University of Belgrade and in few places in England. It relies on mySQL database and CDL package. As I am developing myStructure I am keen to see it being used as much as possible and would be grateful to hear from you if you are interested to use it (it is free) and what in your opinion is missing. For those interested I can send you Word documents on myStructure Design Specification, Functional SPecification and Installation instructions. Looking forward to hearing from you Kind regards DK From owner-chemistry@ccl.net Mon Nov 27 12:46:01 2006 From: "Eric Breynaert Eric.breynaert###biw.kuleuven.be" To: CCL Subject: CCL:G: Gaussian03 Error: Density matrix is not changing but DIIS error Message-Id: <-33086-061127112920-11458-Kl01VlEHp8eEFup/UG5MPg=-=server.ccl.net> X-Original-From: "Eric Breynaert" Date: Mon, 27 Nov 2006 11:29:19 -0500 Sent to CCL by: "Eric Breynaert" [Eric.breynaert]=[biw.kuleuven.be] Hello all, I'm trying to optimize a transition metal structure using DFT ub3lyp LANL2DZ basisset for the metal center , 6-31G(d) for all other elements o.a. O, H, C, S, .... In most cases the optimisation succeeds. But sometimes g03 generates the following error after about 20 to 80 steps in the optimisation. Density matrix is not changing but DIIS error= 2.02D-05 CofLast= 3.35D-01. The SCF is confused. I've already btried different approaches to get arround this but nothing has succeeded. For example, recalculating force constants on the geometry obtained 1 or 2 steps before the error. Forcing g03 to make a new guess at every step of the optimisation using guess=(mix,always). Has anyone encountered such a problem before, or do you know a solution to it ? Thanks, Kind Regards, Eric From owner-chemistry@ccl.net Mon Nov 27 13:21:01 2006 From: "Chandrika J Moudgal moudgal.chandrika{:}epa.gov" To: CCL Subject: CCL: Virulence Factor Activity Relationships (VFARs) Message-Id: <-33087-061127121312-17220-HFJhX14hVy6om0GUbdiRiw-$-server.ccl.net> X-Original-From: "Chandrika J Moudgal" Date: Mon, 27 Nov 2006 12:13:12 -0500 Sent to CCL by: "Chandrika J Moudgal" [moudgal.chandrika],[epa.gov] Hello, Can anyone in the list provide some info with respects to Virulence Factor Activity Relationships (VFARs)? I am looking for a good definition and what the current state of the science is. Also looking for recommendations to apply VFARs to microbial risk assessment to fill in data gaps that are often seen while conducting a microbial risk assessment. A list of related articles will also be much appreciated. Thank you. Chandrika Moudgal From owner-chemistry@ccl.net Mon Nov 27 14:39:00 2006 From: "Nuno A. G. Bandeira nuno.bandeira:_:ist.utl.pt" To: CCL Subject: CCL:G: Gaussian03 Error: Density matrix is not changing but DIIS error Message-Id: <-33088-061127143334-23330-uW/xQ0noPpIXXjXpDupVCA .. server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 27 Nov 2006 19:33:24 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira(~)ist.utl.pt] Eric Breynaert Eric.breynaert###biw.kuleuven.be wrote: > I'm trying to optimize a transition metal structure using DFT ub3lyp LANL2DZ basisset for the metal center , 6-31G(d) for all other elements o.a. O, H, C, S, .... > > In most cases the optimisation succeeds. But sometimes g03 generates the following error after about 20 to 80 steps in the optimisation. > > Density matrix is not changing but DIIS error= 2.02D-05 CofLast= 3.35D-01. > The SCF is confused. Change the SCF converger to either SD, Quadratic or Fermi. The default DIIS can't seem to handle it. This usually happens in tough cases. Regards, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student ],[ IST,Lisbon -- From owner-chemistry@ccl.net Mon Nov 27 15:13:00 2006 From: "Andrew D. Fant fant%%pobox.com" To: CCL Subject: CCL: Gromacs vs NAMD for lipid bilayer simulations Message-Id: <-33089-061127124500-3961-8/WzycO4goSwA5htEffBXA^_^server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 27 Nov 2006 11:27:32 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant**pobox.com] Morning All, I'm looking some rough structural predictions of a membrane embedded protein, and want to do some refinement/relaxation of some of the models to see if I can get a known ligand to come somewhere close to binding. Since I have the time and the cycles, it seems that the proper approach is to set up the protein in a lipid bilayer and soak the sides down. At this point, I have access to Gromacs and NAMD for the simulation. Since I am relatively new to this sort of simulation, I don't have any particular bias about which application to use. I realize that the forcefield selection is probably much more relevant to the quality of the results, but I wouldn't mind if anyone who has more hands-on experience in simulating these systems would chime in with an opinion of which application is likely to yield better results, or at least less likely to make me want to throw up my hands in despair. Thanks in advance, Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant[A]pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Mon Nov 27 16:55:00 2006 From: "Erika Constantino erika+*+klingon.uab.es" To: CCL Subject: CCL:G: problems with SCF Message-Id: <-33090-061127054121-1150-5F98/mJlgqFMGxf349dedw_-_server.ccl.net> X-Original-From: "Erika Constantino" Date: Mon, 27 Nov 2006 05:41:18 -0500 Sent to CCL by: "Erika Constantino" [erika*klingon.uab.es] Good morning, I am doing some calculations on Co(II)-lysine systems, but I sometimes end with the following Gaussian error: "Density matrix is not changing but DIIS error= 1.07D-06 CofLast=-2.52D+00. The SCF is confused." I have been traying to solve it, but I still have some problems with it. I would be very glad if you could give me some help. Thank you very much, Erika Constantino UAB University From owner-chemistry@ccl.net Mon Nov 27 18:53:00 2006 From: "Ibrahim M. Moustafa ria2!^!psu.edu" To: CCL Subject: CCL: GROMACS installation on Mac-OS Message-Id: <-33091-061127175703-7773-np682dmazBtaH+HZ5HzWuw|-|server.ccl.net> X-Original-From: "Ibrahim M. Moustafa" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 27 Nov 2006 17:19:13 -0500 Mime-Version: 1.0 Sent to CCL by: "Ibrahim M. Moustafa" [ria2!=!psu.edu] Dear CCL members, I have a limited experience in Molecular modelling of protein structures; I'd love to expand my experience in that direction. So, I have few questions for people with more experience in the field. I wanted to install GROMACS package on my Mac-OS 10.4 according to the instructions on the GROMACS website. First, I installed the FFTW source as instructed in the README file. Then, I installed the GROMACS binary for the MacOS-X 10.4. However, it did not work! I tried the examples provided with the package but I got "Segmentation faults"....nothing in the output. Just a blank pages while the script is running interactively. I tried to build the package myself from the source code; but again I got the same error message when running the examples' scripts! Presumably, my installation was not successful! even running the command pdb2gmx gives that error message "Segmentation fault"!!! The exact way I did the package building is as follows: 1) compile and install FFTW-3.0.1 in a single precision ./configure --enable-float --enable-type-prefix make make install 2) Compile and install FFTW-3.0.1 in double precision ./configure --enable-type-prefix make make install 3) unpack gromacs-3.3.1.tar; then compile and install ./configure make make install 4) Compile and install FFTW-3.0.1 in double precision again (I was not sure of this step....but whether I did this or not, the results are the same! I got this protocol from some website) ./configure --disable-float --program-suffix=d make make install The following libraries were created in /usr/local/lib libfftw3f.la , libfftw3f.a, libfftw3.la, libfftw3.a (NO dynamic shared library was created) I'd be appreciating if someone of the Experts can guide me through the proper installation of GROMACS on my Mac. Also, I want to ask whether I need to install anything else to do molecular modelling (minimization, MD...etc on protein structures) using this package?? I have another related issue to ask about. I managed to get TINKER to work on my machine; I'd love to ask the professional modelers what do they think of TINKER as a modelling package vs. GROMACS? Some googling on TINKER gave me the feelings that it works for educational purposes; for those who wants to do some modelling using TINKER, probably it needs some modification of the provided code. I'd love to hear your precious comments on that too. thanks for help. Best regards, Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. 201 Althouse Lab. University Park, PA16802 Tel (814) 863 8703 Fax (814) 865 7927 From owner-chemistry@ccl.net Mon Nov 27 22:24:01 2006 From: "Rick Venable venabler(-)nhlbi.nih.gov" To: CCL Subject: CCL: GROMACS installation on Mac-OS Message-Id: <-33092-061127215410-28291-EYqXH5q29MT+r7VVkf+EGQ*o*server.ccl.net> X-Original-From: Rick Venable Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Mon, 27 Nov 2006 21:06:03 -0500 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler(_)nhlbi.nih.gov] There can be issues with the gcc and g77 versions under MacOS X; in particular, if you've kept up to date with OS patches, you may need to download a newer version of the Xcode tools from the Apple Developer site. I had some problems compiling CHARMM until I updated my Xcode tools. -- Rick Venable 29/500 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-8014 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov > Sent to CCL by: "Ibrahim M. Moustafa" [ria2!=!psu.edu] > > I have a limited experience in Molecular modelling of protein > structures; I'd love to expand my experience in that direction. So, I > have few questions for people with more experience in the field. > I wanted to install GROMACS package on my Mac-OS 10.4 according to > the instructions on the GROMACS website. > First, I installed the FFTW source as instructed in the README > file. Then, I installed the GROMACS binary for the MacOS-X 10.4. > However, it did not work! I tried the examples provided with the > package but I got "Segmentation faults"....nothing in the output. > Just a blank pages while the script is running interactively. > I tried to build the package myself from the source code; but again I > got the same error message when running the examples' scripts! > Presumably, my installation was not successful! > even running the command pdb2gmx gives that error message > "Segmentation fault"!!!