From owner-chemistry@ccl.net Mon Sep 24 05:43:00 2007 From: "Sarah Kebbell sarah.kebbell2#%#mail.dcu.ie" To: CCL Subject: CCL:G: Gaussian LogP calculation Message-Id: <-35236-070921094031-25662-qeYIX9VRTuRenK4mELML8g ~~ server.ccl.net> X-Original-From: "Sarah Kebbell" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-15" Date: Fri, 21 Sep 2007 13:58:40 +0100 MIME-Version: 1.0 Sent to CCL by: "Sarah Kebbell" [sarah.kebbell2]-[mail.dcu.ie] Hi there, just wondering if anybody has tried performing a 'logP' calculation in Ga= ussian. There are no options to solvate a molecule in octanol, just enquiring if anybody out there written a solvent parameter file for octanol that could= be loaded into Gaussian to perform such a calculation? Many thanks, Sarah Sarah Kebbell XG36, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9 Ph: +353-1-700-5731 From owner-chemistry@ccl.net Mon Sep 24 08:43:00 2007 From: "Andreas Klamt klamt[a]cosmologic.de" To: CCL Subject: CCL:G: Gaussian LogP calculation Message-Id: <-35237-070924075815-19449-3m8AiSjCiSy584UCtvCixg!^!server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 24 Sep 2007 13:01:29 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt++cosmologic.de] Hi Sarah, quantitative differential solvation between two solvents quite definitely goes beyond the capabilities of simple dielectric continuum solvation models as they are implemented in Gaussian. If you want to calculate logP based on higher level quantum chemistry you can use my COSMO-RS method, which is a statistical thermodynamics of interacting molecular surfaces based on the polarization charge densities resulting > from DFT/COSMO calculations. For more details see the literature references on on our homepage www.cosmologic.de, or my book "COSMO-RS: From quantum chemistry to fluid phase thermodynamics and drug design", Elsevier, 2005. The underlying DFT/COSMO calculations are best done using TURBOMOLE, but older versions of GAUSSIAN03 can be used as well (Mike Frisch has removed the capability to write COSMO-RS compatible COSMO files in the latest subreleases!). In a second step you have to use our COSMOtherm program in order to do the thermodynamic calculations. Best regards Andreas Sarah Kebbell sarah.kebbell2#%#mail.dcu.ie schrieb: > Sent to CCL by: "Sarah Kebbell" [sarah.kebbell2]-[mail.dcu.ie] > > Hi there, > > just wondering if anybody has tried performing a 'logP' calculation in Gaussian. > There are no options to solvate a molecule in octanol, just enquiring if > anybody out there written a solvent parameter file for octanol that could > be loaded into Gaussian to perform such a calculation? > > Many thanks, > > Sarah > > > > Sarah Kebbell > XG36, > School of Chemical Sciences, > Dublin City University, > Glasnevin, > Dublin 9 > Ph: +353-1-700-5731 > > > > -=his is automatically added to each message by the mailing script =-> > > > > > -- ----------------------------------------------------------------------------- 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 Mon Sep 24 09:18:01 2007 From: "Esther.Kellenberger^pharma.u-strasbg.fr" To: CCL Subject: CCL: PDB structures and associated ligand database Message-Id: <-35238-070924040913-15169-ymKuwTxjX+A+Xj20NYixJA!A!server.ccl.net> X-Original-From: Esther.Kellenberger:-:pharma.u-strasbg.fr Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 24 Sep 2007 09:11:58 +0200 MIME-Version: 1.0 Sent to CCL by: Esther.Kellenberger..pharma.u-strasbg.fr Have a look to our scPDB: http://bioinfo-pharma.u-strasbg.fr/scPDB We have extracted "druggable" binding sites from the PDB. The database =20 is fully annotated and non redundant. The current version contains 4300 entries. Next release coming soon =20 (Oktober 2007). Protein and bound ligand coordinates are stored in separate MOL2 =20 files. Hydrogen positions of both molecules have been set in order to =20 optimize interactions in the complexe (see IFP file for the ligand). Protein site and protomol (for docking using Surflex) are available too. You can search the database using protein and/or ligand features or =20 download the full database. reference: J. Chem. Inf. Model., 46 (2), 717 -727, 2006 --=20 Dr. Esther Kellenberger UMR 7175-LC1 74, route du Rhin, B.P.24 F-67401 Illkirch phone: +33 (0)3 90 24 42 21 fax: +33 (0)3 90 24 43 10 www:http://bioinfo-pharma.u-strasbg.fr "Rajarshi Guha rguha|*|indiana.edu" a =E9crit=A0: > > Sent to CCL by: Rajarshi Guha [rguha**indiana.edu] > Hi, I am looking for a database that contains protein structures from > PDB that are associated with a bound ligand. I know I could download > the PDB and process the structures, but I did a literature search > turned up PDB-Ligand (published in Nuc. Acids Res. > http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D238). > > However, all their email addresses are bouncing. Does anybody know how > I could get in touch with the authors or whether there are alternatives > to PDB-Ligand? > > Thanks > > ------------------------------------------------------------------- > Rajarshi Guha > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > All science is either physics or stamp collecting. > =09-- Ernest Rutherford > > > > -=3D This is automatically added to each message by the mailing script =3D= -http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Mon Sep 24 09:53:01 2007 From: "Oscar Olvera Neria oscolv+*+yahoo.com.mx" To: CCL Subject: CCL: AIMPAC with makefiles? Message-Id: <-35239-070921184622-3318-meC3g8npnRouv/3MAnwigw/a\server.ccl.net> X-Original-From: Oscar Olvera Neria Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 21 Sep 2007 16:46:05 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: Oscar Olvera Neria [oscolv,yahoo.com.mx] If you want to compile AIMPAC from McMaster U download site, you must to see the next webpage: http://www.fismol.org/quantum/quantum/aimpac.htm If there is any question, write me Oscar --- "Andrew T Pudzianowski andrew.pudzianowski ~~ bms.com" escribió: > > Sent to CCL by: Andrew T Pudzianowski > [andrew.pudzianowski|bms.com] > Hello, all. There was a query back in 2001 on this > topic but I'm > wondering if there's anything more up to date since > then. Does anyone > have the AIMPAC programs from the McMaster U > download site in some form > that might be workable in a Linux environment? > Please just reply to me > directly if that's more convenient. Otherwise, I'm > sure there are lots > of others who might be interested, and I'd be glad > to summarize any > replies. Cheers....Andrew > > -- > ---------------------------------------------------------------------------------------------- > Andrew T. Pudzianowski, Ph.D. > Computer-Aided Drug Design > Bristol-Myers Squibb R & D > Box 4000 > Princeton NJ 08543-4000 > office: (609) 252-4248 > fax : (609) 252-6030 > ))))))))))))))))))))))))))))))))))))))))))))) > > I used to shave with Ockham's razor > but I kept getting Dedekind cuts. > > ((((((((((((((((((((((((((((((((((((((((((((( > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the -*- > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST-*-ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > ____________________________________________________________________________________ ¡Sé un mejor asador! Aprende todo sobre asados. http://mx.yahoo.com/promos/mejorasador.html From owner-chemistry@ccl.net Mon Sep 24 10:35:01 2007 From: "Greg Warren greg * eyesopen.com" To: CCL Subject: CCL: PDB structures and associated ligand database Message-Id: <-35240-070924092114-30871-7lXsYbiiytIt9iVxJYPwiQ*server.ccl.net> X-Original-From: Greg Warren Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 24 Sep 2007 06:29:40 -0600 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg!A!eyesopen.com] There is a subset of the data you are seeking - PDB bind generated by Shaomeng Wang's group - that is all the structures with bound ligands that have binding affinity data for the ligand. There are two links http://www.pdbbind.org http://sw16.im.med.umich.edu/databases/pdbbind/index.jsp The first link directs you to the second. regards, Greg Warren Rajarshi Guha rguha|*|indiana.edu wrote: > > Sent to CCL by: Rajarshi Guha [rguha**indiana.edu] > Hi, I am looking for a database that contains protein structures from > PDB that are associated with a bound ligand. I know I could download > the PDB and process the structures, but I did a literature search > turned up PDB-Ligand (published in Nuc. Acids Res. > http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D238). > > However, all their email addresses are bouncing. Does anybody know how > I could get in touch with the authors or whether there are > alternatives to PDB-Ligand? > > Thanks > > ------------------------------------------------------------------- > Rajarshi Guha > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > All science is either physics or stamp collecting. > -- Ernest Rutherfordhttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- ======================================== Gregory Warren, PhD OpenEye Scientific Software, Inc 9 Bisbee Court, Suite D Santa Fe, NM 87508 (505) 473-7385 ext 50 mailto:greg[-]eyesopen.com ======================================== From owner-chemistry@ccl.net Mon Sep 24 20:46:00 2007 From: "hadi H H hwchems]~[yahoo.com" To: CCL Subject: CCL:G: g03 Message-Id: <-35241-070923233246-24015-UGt1podhaaXxBSBoNzkyUQ,+,server.ccl.net> X-Original-From: "hadi H H" Date: Sun, 23 Sep 2007 23:32:43 -0400 Sent to CCL by: "hadi H H" [hwchems**yahoo.com] Hi all, I am doing some G3 amd MP2 calculations using G03. The problem is the maximum size for each file under linux in my pc is 2 GB and the scratch files for the calculations need more space. I am using %RWF=/scratch/1,1GB,/scratch/2,100MW,...... and it works for some calculations, and not for all. So please, my question is: How can I make the maximum file size under linux unlimitted? Can I split the scratch files to many files with limit size? Can you kindly advise me?? regards From owner-chemistry@ccl.net Mon Sep 24 21:21:00 2007 From: "hadi H H hwchems[-]yahoo.com" To: CCL Subject: CCL: gamess installation Message-Id: <-35242-070923233928-24401-ZHIaj59raBfnasBYgIVd8Q]~[server.ccl.net> X-Original-From: "hadi H H" Date: Sun, 23 Sep 2007 23:39:24 -0400 Sent to CCL by: "hadi H H" [hwchems+*+yahoo.com] Hi all, I want to install GAMESS software but I need for compilation the ((endfile.tar.gz)) for G77 which I can not download from the net. Can you kindly tell me from where I can get this file?? regards From owner-chemistry@ccl.net Mon Sep 24 23:49:01 2007 From: "Bo Peng bopengchemist],[gmail.com" To: CCL Subject: CCL:G: Problem of Frequency job of CI-Single method in G03w Message-Id: <-35244-070924233445-3302-f4LV2Dbs3gGyu38QZflnmg-.-server.ccl.net> X-Original-From: "Bo Peng" Date: Mon, 24 Sep 2007 23:34:41 -0400 Sent to CCL by: "Bo Peng" [bopengchemist_+_gmail.com] Dear CCL subscribers, Recently, I have used the CIS method in G03w to optimize the excited states of a series organic molecules (~50 atoms),whose ground states have been optimized and verified no image frequencies, all the jobs ends normally. Then when I tried to do the frequencies analysis of these optimized excited states, none of them could end normally. The following is the part of the .log file of one of these molecules which has 53 atoms. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ..... Doing CIS second derivatives. from this step, the program try to calculate the analytic second derivative. This link is doing 162 degrees of freedom form MO integral derivatives with frozen-active canonical formalism. CisSec: MDV= 131071680 Frozen orbitals handled with amplitudes over full window. CISAX will form 81 AO SS matrices at one time. Operation on file out of range. report errors!!! FileIO: IOper= 1 IFilNo(1)=-19990 Len= 0 IPos= 5183919 Q= 7 98532104 dumping /fiocom/, unit = 1 NFiles = 121 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 799475200 FType=2 FMxFil=10000 Number 0 0 0 0 0 0 0 0 Base 455111872 8375649 13073128 5901824 6582272 9276928 31812096 1136640 End 455112192 8375808 13073408 5903360 6583808 9277952 31823872 1137152 End1 455112192 8375808 13073408 5903360 6583808 9277952 31823872 1137152 Wr Pntr 455111872 8375649 13073128 5902336 6582272 9264128 31785472 1136640 Rd Pntr 455111872 8375649 13073128 5902336 6582272 9264128 31785472 1136640 Length 320 159 280 1536 1536 1024 11776 512 Number 0 0 0 0 0 0 0 0 Base 8567808 11201024 9924608 6589440 29226496 13750272 372340736 8439808 End 9176064 12631568 11025920 6800896 31109632 14422528 382064128 8503808 End1 9176064 12631568 11025920 6800896 31109632 14422528 382064128 8503808 Wr Pntr 8375649 11201024 9924608 6589440 24790528 13750272 289794560 8439808 Rd Pntr 8375649 11201024 9924608 6589440 24790528 13750272 289794560 8503807 Length 608256 1430544 1101312 211456 1883136 672256 9723392 64000 ..... dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 65536 FType=2 FMxFil=10000 Number 0 Base 20480 End 65536 End1 65536 Wr Pntr 20480 Rd Pntr 20480 Length 45056 Error termination in NtrErr: NtrErr Called from FileIO. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ the following is the .gjf file: +++++++++++++++++++++++++++++++++++++++++ %rwf=a1,245mw,a2,245mw,a3,245mw,a4,245mw %chk=cc.chk %mem=1000mb %NprocLinda=8 Geom=AllCheck Guess=Read RCIS(Read,direct)/6-31+G(d) freq ++++++++++++++++++++++++++++++++++++++++++ before I send the message to CCL, I have done some GOOGLE searches, like there seems the situations are somewhat different from mine. I have also tried to use freq=numer instead of freq, it seems not very helpful. can anybody give me a favor to analyze what is the problem? how to solve this? any help and hints is really appreciated! Bo Peng Ph. D. candidate Nankai Univ. Tientsin, CHN bopengchemist**gmail.com