From owner-chemistry@ccl.net Mon Sep 25 00:34:28 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id AAA13541; Mon, 25 Sep 1995 00:31:39 -0400 Received: from email.okstate.edu for pran@okstate.edu by bedrock.ccl.net (8.6.10/950822.1) id AAA13234; Mon, 25 Sep 1995 00:31:38 -0400 Received: from rs.ucc.okstate.edu (rs.ucc.okstate.edu [139.78.100.15]) by email.okstate.edu (8.6.12/8.6.12) with SMTP id XAA09683 for ; Sun, 24 Sep 1995 23:31:20 -0500 Date: Sun, 24 Sep 1995 23:31:20 -0500 Message-Id: <199509250431.XAA09683@email.okstate.edu> X-Sender: pran@email.okstate.edu X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: Ran Pan Subject: mopac Dear Netter: I am having some difficulties to make mopac7 or mopac6 run on our DEC-ALPHA workstation. I would appreciate it very much if some experts can give me some suggestions or tips. Please reponse to my E-mail address. Thank you very much for your time and consideration. Sincerely, Ran Pan From smb@smb.chem.niu.edu Mon Sep 25 10:04:38 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.10/950822.1) id JAA18822; Mon, 25 Sep 1995 09:59:06 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA12181 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net>); Mon, 25 Sep 1995 08:59:08 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA22646; Mon, 25 Sep 95 08:48:34 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA17002; Mon, 25 Sep 95 08:44:33 -0500 Date: Mon, 25 Sep 95 08:44:33 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9509251344.AA17002@smb.chem.niu.edu> To: CHEMISTRY@www.ccl.net Subject: ECCC2 Abstracts Due Friday Sep. 29, 1995 On final announcment concerning the abstract deadline for the second electronic computational chemistry conference (ECCC2). Abstracts must be submitted by midnight Friday Sept. 29, 1995 for acceptance into this year's conference. Information on the conference and how to submit an abstract can be found at http://hackberry.chem.niu.edu/ECCC2 Thanks Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From owner-chemistry@ccl.net Mon Sep 25 10:49:37 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA20033; Mon, 25 Sep 1995 10:45:26 -0400 Received: from wugate.wustl.edu for gregory@wucmd.wustl.edu by bedrock.ccl.net (8.6.10/950822.1) id KAA16204; Mon, 25 Sep 1995 10:45:24 -0400 Received: from wucmd by wugate.wustl.edu (8.6.12/8.6.11) with SMTP id JAA08333; Mon, 25 Sep 1995 09:45:24 -0500 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:chemistry@ccl.net id AA29720; Sun, 24 Sep 95 21:16:09 -0500 Date: Sun, 24 Sep 1995 20:29:39 -0500 (CDT) From: Gregory Nikiforovich Subject: Re: CCL:Small Peptide Dynamics To: Charles Martin Cc: chemistry@ccl.net In-Reply-To: <9509242214.AA15634@rainbow.uchicago.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 24 Sep 1995, Charles Martin wrote: > Dawei Lin writes.. > > > > I want to do molecular dynamics calculation of small peptides(lenght 5 > > to 8). Before I set out to do the calculations, I like to listen any of > > your suggests or experences. > ....... > > I would be most interested in reading other opinions and > seeing other pieces of evidence, pro and/or contrary. Anyone? > > Chuck Martin > As I understood the original question, the problem is in performing the comprehensive conformational search for peptides of small size. In my experience, the problem is mainly not in the force field parameters, but in calculation protocols. All of available protocols are not perfect in finding ALL low-energy local minima for a given peptide. However, there is some order, from better to worse: 1) build-up procedures; 2) MD; 3) Monte- Carlo (different options); 4) random generation of conformers; 5) systematic search. The order is based on accuracy of predictions made by calculations plus expences (in terms of computational time). Of course, this is my personal opinion; more in details see my review in Int. J. Pept. Prot. Res., (1994) 44, 513-531. Now, too bad that the build-up procedures are not represented in any available commercial software. I have developed this protocol and I am using it for many years, but this is not a commercial product (at least, yet). If anybody really needs these calcualtions to be done, please feel free to use my e-mail address/phone number listed below. ############################################################################## Gregory V. Nikiforovich Phone (314) 935-4677 Research Professor Fax (314) 935-4979 Center for Molecular Design E-mail address: Washington University gregory@wucmd.wustl.edu Lopata Hall, Box 1099 St.Louis, MO 63130 ############################################################################## From glotov@mbi.FTA-Berlin.DE Mon Sep 25 11:04:39 1995 Received: from cuboid.mbi.fta-berlin.de for glotov@mbi.FTA-Berlin.DE by www.ccl.net (8.6.10/950822.1) id KAA20228; Mon, 25 Sep 1995 10:54:14 -0400 Message-Id: <199509251454.KAA20228@www.ccl.net> Received: from a1pc06.mbi.FTA-Berlin.de by cuboid.mbi.fta-berlin.de with SMTP (1.37.109.4/16.2) id AA17293; Mon, 25 Sep 95 15:50:43 +0100 Comments: Authenticated sender is From: "Aleksei Glotov" To: chemistry@www.ccl.net Date: Mon, 25 Sep 1995 16:46:44 +0000 Subject: pdb format, what is it? Reply-To: glotov@mbi.fta-berlin.de Priority: urgent X-Mailer: Pegasus Mail for Windows (v2.0-WB4) Hi all! Does anybody know what is PDB (Brookhaven Protein Databank) format? I have xyz set of atoms coordinates and try to use Rasmol. Thanks in advance, A. ---------------------------------- Alexei Glotov Max-Born-Institut, Rudower Chaussee 6, Postfach 1107, D 12474 Berlin, Germany phone: (030) 6392 1221 E-mail: glotov@mbi.fta-berlin.de ---------------------------------- From chpajt@bath.ac.uk Mon Sep 25 15:49:41 1995 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.6.10/950822.1) id PAA25770; Mon, 25 Sep 1995 15:35:19 -0400 Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Mon, 25 Sep 1995 20:35:17 +0100 Date: Mon, 25 Sep 1995 20:35:05 +0100 (BST) From: A J Turner To: chemistry@www.ccl.net Subject: Charmm RTF's and G94 - chelp Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Can anyone tell me how to convert from the electrostatic charges from 'CHELP' in G94 to the atom charges in a Charmm RTF? I have looked for some hours at the papers and on-line manual - and simply cannot find what units Charmm is using (plus - lacking a G94 manual does not help!). Thanks in anticipation Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From kostov@rainbow.uchicago.edu Mon Sep 25 18:34:43 1995 Received: from midway.uchicago.edu for kostov@rainbow.uchicago.edu by www.ccl.net (8.6.10/950822.1) id SAA28627; Mon, 25 Sep 1995 18:26:57 -0400 Received: from rainbow.uchicago.edu (rainbow.uchicago.edu [128.135.136.33]) by midway.uchicago.edu (8.6.10/8.6.4) with SMTP id RAA0\ 8221 for <@midway.uchicago.edu:chemistry@www.ccl.net>; Mon, 25 Sep 1995 17:26:57 -0500 Received: by rainbow.uchicago.edu (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@www.ccl.net id AA26119; Mon, 25 Sep 95 17:26:34 -0500 Date: Mon, 25 Sep 95 17:26:34 -0500 From: kostov@rainbow.uchicago.edu (Konstantin Kostov) Message-Id: <9509252226.AA26119@rainbow.uchicago.edu> To: chemistry@www.ccl.net Subject: Formats of binary CHARMM files Dear Netters, I need to read some binary files created with CHARMM. Could someone tell me the formats of *.CRD, *.DCD and *.DVL files. I would also appreciate any reference to existing programs that convert the CHARMM binary files to ACSII. Thanks, Konstantin kostov@rainbow.uchicago.edu