From chemistry-request@server.ccl.net Thu Oct 26 13:10:06 2000 Received: from compchem.dfh.dk (compchem.dfh.dk [130.225.225.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA19947 for ; Thu, 26 Oct 2000 13:10:04 -0400 Received: (from jeremy@localhost) by compchem.dfh.dk (SGI-8.9.3/8.9.3) id TAA52579 for chemistry@ccl.net; Thu, 26 Oct 2000 19:07:55 +0200 (MEST) Date: Thu, 26 Oct 2000 19:07:54 +0200 From: Jeremy Greenwood To: chemistry@ccl.net Subject: Gaussian: recalculating thermochem Message-ID: <20001026190754.A1254620@compchem.dfh.dk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i Gaussian allows the rapid recalculation of thermochemical data (e.g. with new scaling factor, temp., pressure) from the checkpoint file after a frequency job using freq=readfc However, if the checkpoint file is missing, it gets more tricky. We would like to recalculate the thermochemistry without having to resort to re-running the frequency job. A checkpoint file can be created by a single point calculation. The force constants are listed in the archive, and can be read in using opt=fccards, or by editing the formatted checkpoint file by hand and unformatting, but this doesn't seem sufficient to convince Gaussian to perform freq=readfc. One could use the information in the output file to recalculate the thermochemistry from first principles, but this is a little laborious. It would be nice to have an automated procedure. Does someone have a good way to do this? Thanks in advance, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy.greenwood@i.am Department of Medicinal Chemistry ph +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ---------------------------------------------------------------------- On two occasions I have been asked [by members of Parliament!], 'Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?' I am not able rightly to apprehend the kind of confusion of ideas that could provoke such a question. -- Charles Babbage ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Oct 25 20:09:42 2000 Received: from mail2.ceniai.inf.cu (mail2.ceniai.inf.cu [169.158.128.151]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA15134 for ; Wed, 25 Oct 2000 20:09:33 -0400 Received: from uucp.ceniai.inf.cu ([169.158.128.157]) by mail2.ceniai.inf.cu (8.9.3/8.9.3) with ESMTP id TAA27068 for ; Wed, 25 Oct 2000 19:55:37 -0500 (EST) Received: (from uucp@localhost) by uucp.ceniai.inf.cu (8.9.3/8.9.3) with UUCP id UAA79868 for chemistry@ccl.net; Wed, 25 Oct 2000 20:11:18 -0500 (EST) X-POP3-RCPT: chemistry@ccl.net X-RCPT-TO: chemistry@ccl.net Received: from oxidacioncat ([192.168.1.207]) by hermes.ceinpet.inf.cu (8.8.7/8.8.7) with SMTP id JAA03052 for ; Wed, 25 Oct 2000 09:57:59 -0500 Message-Id: <200010251457.JAA03052@hermes.ceinpet.inf.cu> From: "Alejandro Gonzalez Peralta" To: chemistry@ccl.net Date: Wed, 25 Oct 2000 14:58:32 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Subject: basis set needed... Priority: normal Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by server.ccl.net id UAA15135 Hi all: I'm starting a study on mixed oxides, specifically oxides of the ABOx kind, using Hartree Fock calculations. I'd appreciate it if someone could help with references or ideas about basis set for atoms of atomic number greater than 54, (example: La). Alejandro G. Peralta -------------------------------------------------------- Unidad de Catálisis. CEINPET Washington #169, esq. Churruca. Cerro 12000 Ciudad Habana. Cuba -------------------------------------------------------- From chemistry-request@server.ccl.net Wed Oct 25 23:23:38 2000 Received: from mta4.263.net ([202.96.44.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA15791 for ; Wed, 25 Oct 2000 23:23:36 -0400 Received: by mta4.263.net (Postfix, from userid 60001) id A1FD61C7253CB; Thu, 26 Oct 2000 11:28:44 +0800 (CST) MIME-Version: 1.0 Message-Id: <39F7A4EC.23044@mta4> Date: Thu, 26 Oct 2000 11:28:44 +0800 (CST) From: zkcfx@263.net To: chemistry@ccl.net Subject: why H disappear Dear CCLers: I now make it clearer what happens.Any handy help would be appreciated. for example,if I use PM3 to optimize H-Ph-CC-H and NH3. Then I use MOLDEN3.6 to read the output, though the image show the white H atoms, in the Z-matrix it disappear. If I write it into a file using XYZ,then the H will appear in my file. But anyway they will not show in the Z-matrix window. However, if I use MOVE, I can see some steps of the optimization process will have H atoms appear. The error message for Molden is :error in automatic cartesian-z-matrix conversion. the number of writen atoms is not equal to selected atoms. From chemistry-request@server.ccl.net Thu Oct 26 14:19:45 2000 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA20406 for ; Thu, 26 Oct 2000 14:19:45 -0400 Received: from localhost (renxiao@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id LAA19932 for ; Thu, 26 Oct 2000 11:19:46 -0700 (PDT) X-Authentication-Warning: neon.chem.ucla.edu: renxiao owned process doing -bs Date: Thu, 26 Oct 2000 11:19:45 -0700 (PDT) From: Renxiao Wang To: Computational Chemistry List Subject: Looking for Ki/Kd values Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, You know there are so many protein/ligand complexes now available in PDB. I believe that, for many of them, the Ki/Kd (or IC50 ...) values have been determined experimentally. Does anybody have idea where to find a summary of such information? Needless to mention, such information is very important for analyzing receptor/ligand interactions. I know a few papers which list some (PDB code + Ki/Kd): o Eldridge et al. J.Comput.-Aided Mol.Des. 1997, 11, 425-445. o Bohm, J.Comput.-Aided Mol.Des. 1998, 12, 309-323. o Kuntz et al. Proc.Natl.Acad.Sci. 1999, 96, 9997-10002. Definitely they are not complete. So if you know something else, please let us know. I will put back the summary. Thanks a lot! Renxiao Wang From chemistry-request@server.ccl.net Thu Oct 26 15:28:56 2000 Received: from avfw98.lundbeck.com (firewall.lundbeck.com [130.227.160.11]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA20949 for ; Thu, 26 Oct 2000 15:28:56 -0400 Received: from firewall.lundbeck.com [130.227.160.11] (HELO localhost) by avfw98.lundbeck.com (AltaVista Mail V2.0J/2.0J BL25J listener) id 0000_005e_39f8_90fc_48a0; Thu, 26 Oct 2000 21:15:56 +0100 Received: from somewhere by smtpxd Sender: torleif@ccl.net Message-ID: <39F882CD.8506CF68@lundbeck.com> Date: Thu, 26 Oct 2000 21:15:25 +0200 From: Torleif alternative account To: Renxiao Wang , chemistry@ccl.net Subject: Re: CCL:Looking for Ki/Kd values References: Dear Renxiao, I can recommend the initiative by Michael Gilson at CARB to compile all of this data: http://www.bindingdb.org. Regards -- Jan Dr. Jan T. Pedersen H. Lundbeck A/S Ottiliavej 9 2500 Valby Copenhagen, Denmark phone : +45 36 44 24 25 ext 2887 email: jatp@lundbeck.com Renxiao Wang wrote: > Dear all, > > You know there are so many protein/ligand complexes now available in PDB. > I believe that, for many of them, the Ki/Kd (or IC50 ...) values have been > determined experimentally. Does anybody have idea where to find a summary > of such information? > > Needless to mention, such information is very important for analyzing > receptor/ligand interactions. I know a few papers which list some (PDB > code + Ki/Kd): > > o Eldridge et al. J.Comput.-Aided Mol.Des. 1997, 11, 425-445. > o Bohm, J.Comput.-Aided Mol.Des. 1998, 12, 309-323. > o Kuntz et al. Proc.Natl.Acad.Sci. 1999, 96, 9997-10002. > > Definitely they are not complete. So if you know something else, please > let us know. I will put back the summary. Thanks a lot! > > Renxiao Wang