From chemistry-request@server.ccl.net Sat Nov 25 04:00:44 2000 Received: from hotmail.com (f310.law7.hotmail.com [216.33.236.188]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA19027 for ; Sat, 25 Nov 2000 04:00:44 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sat, 25 Nov 2000 00:58:37 -0800 Received: from 202.54.80.218 by lw7fd.law7.hotmail.msn.com with HTTP; Sat, 25 Nov 2000 08:58:36 GMT X-Originating-IP: [202.54.80.218] From: "Seth John" To: chemistry@ccl.net Subject: How do I find a database of amino acid input-files for MOPAC? Date: Sat, 25 Nov 2000 08:58:36 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 25 Nov 2000 08:58:37.0180 (UTC) FILETIME=[E5DF53C0:01C056BD] I need to find a place to download input files for proteins, sugars, and other biological molecules. I either need this information in MOPAC format, or some format that is convertible to MOPAC format with Babel. I know this is a basic question, but I'm writing some programs alone in India and can't find this anywhere on the web. (I'm on a one year Fulbright grant studying watershed management as a break from chemistry in the US!) -Seth John sethjohn@hotmail.com _____________________________________________________________________________________ Get more from the Web. FREE MSN Explorer download : http://explorer.msn.com From chemistry-request@server.ccl.net Sat Nov 25 18:02:33 2000 Received: from fischer.pharm.uu.nl (fischer.pharm.uu.nl [131.211.56.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA23065 for ; Sat, 25 Nov 2000 18:02:32 -0500 Received: from fischer (localhost [127.0.0.1]) by fischer.pharm.uu.nl (SGI-8.9.3/8.9.3) with ESMTP id AAA89688 for ; Sun, 26 Nov 2000 00:02:30 +0100 (MET) Message-Id: <200011252302.AAA89688@fischer.pharm.uu.nl> To: chemistry@ccl.net Reply-To: Malcolm Gillies Subject: CHARMM19 protein parameters in TINKER format? Date: Sun, 26 Nov 2000 00:02:30 +0100 From: Malcolm Gillies I'm looking for the CHARMM19 (polar hydrogen) protein parameter set converted into TINKER prm format. I'd like to compare some simulations using CHARMM22 (all atom) to the polar-H equivalent. TINKER does include some OPLS parameters, but the form of the improper terms is different to in CHARMM. Thanks in advance. cheers, Malcolm Gillies -- Malcolm Gillies PhD student, computational medicinal chemistry Dept Medicinal Chemistry, Faculty of Pharmacy, Utrecht University, The Netherlands From chemistry-request@server.ccl.net Sat Nov 25 22:05:46 2000 Received: from keeper.ludwig.edu.au (keeper.ludwig.edu.au [128.250.250.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA23888 for ; Sat, 25 Nov 2000 22:05:44 -0500 Received: by keeper.ludwig.edu.au with Internet Mail Service (5.5.2650.21) id ; Sun, 26 Nov 2000 14:05:17 +1100 Message-ID: <805AD25D3702D311805900062B004E42BD0923@keeper.ludwig.edu.au> From: Robert Jorissen To: "'chemistry@ccl.net'" Subject: RE: help with MMFF94 in CHARMM (solution) Date: Sun, 26 Nov 2000 14:05:11 +1100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers I seem to have found a solution my problem and am posting my solution as a courtesy to anyone who may have a similar problem. My problem was: when using the MMFF94 forcefield in CHARMM, I could not reproduce the non-bonded energies of molecules in the MMFF94 validation set (see http://www.ccl.net/cca/data/MMFF94/). As Rebecca Rone suggested, the problem was with some of the parameters. The default VDW cut-off is 8 Angstroms when MMFF94 is used. This cut-off should be set to a number larger than the molecule's largest dimension. Similarly, the treatment of electrostatic energies requires a change in parameter. The default MSHIFt keyword should be replaced by the TRUNCation keyword. The following example script (adapted from one of the CHARMM test scripts) illustrates this: * BEWCUB.inp * Test reading in one small molecule structure in .mrk format and calculating * its energy in CHARMM * ! Set up MMFF94 forcefield for use set 0 /p1/charmm/test/data/ ! input data directory stream @0mmff_setup.str ! Read and generate the small molecule open read form unit 1 name "BEWCUB.mrk" read merck unit 1 close unit 1 generate write merck unit 6 ! Calculate the MMFF energy of the molecule update inbfrq 1 ihbfrq 0 CUTNB 999. CTOFNB 888. cdie e14fac 0.75 CTVTRN 888. TRUNC energy stop The CTVTRN 888. (VDW cut-off) and TRUNC (handling of long range electrostatics) parts of the update command were the additions that seemed to make everything work. I have only tested a small portion of the MMFF94 validation set and so there may be further problems I haven't picked up. Robert Jorissen Ludwig Institute for Cancer Research