From rvenable&$at$&deimos.cber.nih.gov Mon Jun 29 16:26:39 1998 Received: from deimos.cber.nih.gov (deimos.cber.nih.gov [128.231.52.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA26492 Mon, 29 Jun 1998 16:26:38 -0400 (EDT) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA277391928; Mon, 29 Jun 1998 16:25:28 -0400 Date: Mon, 29 Jun 1998 16:25:28 -0400 (EDT) From: Rick Venable Reply-To: Rick Venable To: Chris Jao Cc: CHEMISTRY -8 at 8- www.ccl.net Subject: Re: CCL:G:parameter for sulfoxide In-Reply-To: <199806291816.NAA04864:~at~:stanley.bio.purdue.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 29 Jun 1998, Chris Jao wrote: > I am using CHARMm all hydrogen forcefield and need to know the > parameters for sulfoxide, Can anyone kindly tell me where I can find > it or how I can get it by doing ab initio calculation? > ps. I did an optimization of CH3CH2S(=O)CH3 calculation using g94 > (HF/6-31G**) and I really don't know what to do with it. In general, one uses experimental geometries, with bond and angle force constants from IR spectroscopy; ab initio calculations are used to derive partial charges, perhaps at several geometries, and can be used to refine the LJ parameters. Note that for sp2 hydridized carbon, one often uses an added improper torsion to enforce planarity. The results should be iteratively refined against e.g. a crystal structure at a minimum. There's the CHARMm force field distributed by MSI for use with the Quanta/CHARMm product; I don't know if their parameter development methodology has been published. Also, their force field has been "generalized" in order be used for a wider range of polymers, but I've done some carbohydrate simulations which suggest the parameters may not be as transferable as one would like. Check the MSI manuals, or contact someone from MSI for development details; perhaps a reader of CCL has some experiences to share... There's also the CHARMM force fields developed by Alex MacKerell and collaborators; these are the ones distributed with the academic version from Harvard, and are specific for each biopolymer type. A couple papers on the methodology are: Pavelites JJ, Gao JL, Bash PA, et al. A molecular mechanics force field for NAD(+), NADH, and the pyrophosphate groups of nucleotides J COMPUT CHEM 18: (2) 221-239 JAN 30 1997 Yin DX, Mackerell AD Combined ab initio empirical approach for optimization of Lennard-Jones parameters J COMPUT CHEM 19: (3) 334-348 FEB 1998 -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable \\at// deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) http://www.erols.com/rvenable