From chemistry-request@ccl.net Thu Jan 29 00:47:51 2004 Received: from chemdept.chem.ou.edu (chemdept.chem.ou.edu [129.15.12.110]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i0T5loU6004207 for ; Thu, 29 Jan 2004 00:47:50 -0500 Received: from [129.15.13.131] (HELO orchid) by chemdept.chem.ou.edu (Stalker SMTP Server 1.8b8) with SMTP id S.0000847614 for ; Wed, 28 Jan 2004 23:59:49 -0600 From: "Asif Rahaman" To: Subject: how to calculate the solvation free energy calculation using PCM Date: Wed, 28 Jan 2004 23:49:41 -0600 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers: I am trying to calculate the solvation free energy for methane in water. I have used Gaussian 03's PCM model. I get the following results: -------------------------------------------------------------------- Variational PCM results ======================= (a.u.) = -40.533741 (a.u.) = -40.533856 Total free energy in solution: with all non electrostatic terms (a.u.) = -40.522765 -------------------------------------------------------------------- (Polarized solute)-Solvent (kcal/mol) = -.07 -------------------------------------------------------------------- Cavitation energy (kcal/mol) = 9.98 Dispersion energy (kcal/mol) = -3.07 Repulsion energy (kcal/mol) = .06 Total non electrostatic (kcal/mol) = 6.96 -------------------------------------------------------------------- Now how do I cal calculate the solvation free energy from the above table? Is it ( - ) or I have to perform the gas phase calculation and then subtract the gas phase energy > from the solution phase energy. With best regards, Asif I use the following input: $ RunGauss %NProc=4 %chk=ch4 %mem=64MB # b3lyp/6-311g** opt pop=chelpg scrf=(pcm, solvent=water) Methane B3LYP/6-311G** 0 1 C1 H1 1 b1 H2 1 b1 2 a1 H3 1 b1 2 a1 3 d1 1 H4 1 b1 2 a1 4 d1 1 b1 1.1 a1 109.5 d1 109.5 SAS EPS=78.5 BONDI DENSITY=1.000 TABS=298.0 From chemistry-request@ccl.net Thu Jan 29 02:34:37 2004 Received: from adrik.bchs.uh.edu (Adrik.BCHS.uh.edu [129.7.238.220]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0T7YaU6010437 for ; Thu, 29 Jan 2004 02:34:36 -0500 Received: from adrik.bchs.uh.edu (localhost [127.0.0.1]) by adrik.bchs.uh.edu (8.12.10/8.12.10) with ESMTP id i0T6nsUi399310 for ; Thu, 29 Jan 2004 06:49:54 GMT Received: from localhost (jebalunode@localhost) by adrik.bchs.uh.edu (8.12.10/8.12.5/Submit) with ESMTP id i0T6noL9403167 for ; Thu, 29 Jan 2004 01:49:54 -0500 (CST) Date: Thu, 29 Jan 2004 01:49:50 -0500 From: Jerry Ebalunode cc: chemistry|at|ccl.net Subject: Volumes calculated by PASS In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all, Does any one know the units for the volume calculated by the PASS program for cavitities present in proteins? From chemistry-request@ccl.net Thu Jan 29 06:16:55 2004 Received: from csiromail3.act.csiro.au (csiromail3.act.csiro.au [152.83.2.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0TBGrU6023648 for ; Thu, 29 Jan 2004 06:16:53 -0500 Received: from csiromail7.act.csiro.au (unknown [152.83.2.18]) by localhost.csiro.au (Postfix) with ESMTP id D78CD1382A0; Thu, 29 Jan 2004 11:18:50 +0000 (UTC) Received: from csiromail7.act.csiro.au (localhost.localdomain [127.0.0.1]) by localhost.act.csiro.au (Postfix) with ESMTP id 6316473535; Thu, 29 Jan 2004 22:12:49 +1100 (EST) Received: from csiromail1.vic.csiro.au (csiromail1.vic.csiro.au [138.194.2.12]) by csiromail7.act.csiro.au (Postfix) with SMTP id 1520873533; Thu, 29 Jan 2004 22:12:49 +1100 (EST) Received: from [138.194.4.95] (vic095.dialup.csiro.au [138.194.4.95]) by csiromail1.vic.csiro.au (Postfix) with ESMTP id 9B386138005; Thu, 29 Jan 2004 22:18:43 +1100 (EST) In-Reply-To: <3B5A92DA-522A-11D8-BB41-000A957D73C4|at|chemistry.ucsc.edu> References: <3B5A92DA-522A-11D8-BB41-000A957D73C4|at|chemistry.ucsc.edu> Mime-Version: 1.0 (Apple Message framework v612) Content-Type: multipart/alternative; boundary=Apple-Mail-13-431159093 Message-Id: Cc: chemistry|at|ccl.net From: Kim Branson Subject: dock for osx. Date: Thu, 29 Jan 2004 22:18:43 +1100 To: X-Mailer: Apple Mail (2.612) X-Spam-Status: No, hits=0.9 required=7.0 tests=HTML_30_40,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --Apple-Mail-13-431159093 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Hi all, for the many many curious people the steps to compile dock for osx are You need to include before , you need to include in parm.c i.e #include #include #include #include #include "define.h" #include "utility.h" #include "global.h" #include "parm.h" add -lgcc to your link line or link against /usr/lib/libgcc.a. I havent tried compiling with different apple specific gcc and g77 flags yet, or pushing the optimisation. But this does produce a working version of DOCK and GRID. cheers kim On 29/01/2004, at 6:10 PM, wrote: > You need to use > > > > -lcc_dynamic > > > > > If you get it to work, would you be kind enough to send a summary of > what it takes? > > > > Thanks. > > > > > William G. Scott > > > > Associate Professor > > Department of Chemistry and Biochemistry > > and The Center for the Molecular Biology of RNA > > Sinsheimer Laboratories > > University of California at Santa Cruz > > Santa Cruz, California 95064 > > USA > > > > phone: +1-831-459-5367 (office) > > +1-831-459-5292 (lab) > > fax: +1-831-4593139 (fax) > > url: http://chemistry.ucsc.edu/~wgscott/ > > > > > --Apple-Mail-13-431159093 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Hi all, for the many many curious people the steps to compile dock for osx are You need to include < before <, you need to include < in parm.c i.e #include < #include < #include < #include < #include "define.h" #include "utility.h" #include "global.h" #include "parm.h" add -lgcc to your link line or link against /usr/lib/libgcc.a. I havent tried compiling with different apple specific gcc and g77 flags yet, or pushing the optimisation. But this does produce a working version of DOCK and GRID. cheers kim On 29/01/2004, at 6:10 PM, < wrote: You need to use Courier NewFFFF,0000,0000-lcc_dynamic If you get it to work, would you be kind enough to send a summary of what it takes? Thanks. William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) url: http://chemistry.ucsc.edu/~wgscott/ --Apple-Mail-13-431159093-- From chemistry-request@ccl.net Thu Jan 29 10:37:10 2004 Received: from mailhost3.tudelft.nl (mailhost3.tudelft.nl [130.161.180.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0TFb9U6014315 for ; Thu, 29 Jan 2004 10:37:10 -0500 Received: from 127.0.0.1 (localhost [127.0.0.1]) by rav.antivirus (Postfix) with SMTP id 6F6475FC42 for ; Thu, 29 Jan 2004 16:39:06 +0100 (MET) Received: from mail.dct.tudelft.nl (mail.dct.tudelft.nl [130.161.196.201]) by mailhost3.tudelft.nl (Postfix) with ESMTP id 253915FC35 for ; Thu, 29 Jan 2004 16:39:04 +0100 (MET) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); 29 Jan 04 16:39:06 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); 29 Jan 04 16:39:04 +0200 From: "Stefan Bromley" Organization: Delft University of Technology (TNW-DCT) To: chemistry{at}ccl.net Date: Thu, 29 Jan 2004 16:38:54 +0100 MIME-Version: 1.0 Subject: Computational drug discovery Message-ID: <40193718.28471.2E5DCC84@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.12a) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL, I am currently planning a lecture course on the use of computer modelling in drug development. Recently on the CCL there was a question and reply summary concerning drugs that have been discovered via the use of computational methods. I inadvertantly deleted the summary and cannot find it on the archives - could someone please forward it on to me? Also if anyone has any other recommendations for good background material I more be more than happy to know about them. Many thanks, Stefan Bromley ________________________________________________________ Dr Stefan T. Bromley Laboratory of Applied Organic Chemistry and Catalysis DelftChemTech, Delft University of Technology Julianalaan 136, 2628 BL Delft The Netherlands Phone : + 31 1527 89418 e-mail : S.T.Bromley{at}tnw.tudelft.nl ________________________________________________________ From chemistry-request@ccl.net Thu Jan 29 20:10:29 2004 Received: from web60108.mail.yahoo.com (web60108.mail.yahoo.com [216.109.118.87]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i0U1ARU6002435 for ; Thu, 29 Jan 2004 20:10:28 -0500 Message-ID: <20040130011228.81604.qmail=at=web60108.mail.yahoo.com> Received: from [137.131.108.51] by web60108.mail.yahoo.com via HTTP; Thu, 29 Jan 2004 17:12:28 PST Date: Thu, 29 Jan 2004 17:12:28 -0800 (PST) From: Eric Hu Subject: g98 error To: chemistry=at=ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.9 required=7.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi I am doing a frequency calculation with b3lyp/6-31++g**. I got the following error message although I have plenty of disk space: 99 vectors were produced by pass 10. 99 vectors were produced by pass 11. 99 vectors were produced by pass 12. 99 vectors were produced by pass 13. 99 vectors were produced by pass 14. 90 vectors were produced by pass 15. 49 vectors were produced by pass 16. Erroneous write during file extend. write 188415 instead of 4096 Probably out of disk space. Write error in NtrExt1 Eric __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://webhosting.yahoo.com/ps/sb/