Subject: parameter for sulfoxide

From: Chris Jao <[email-masked]>
Date: Mon, 29 Jun 1998 13:16:12 -0500

Hi,
    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?
Thank you very much.
chris
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.

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From: Rick Venable <[email-masked]>
Date: Mon, 29 Jun 1998 16:25:28 -0400 (EDT)

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
[email-masked]  |    \  /  |=|    position of the FDA; for that,
http://nmr1.cber.nih.gov/           \/   |=|    see   http://www.fda.gov  )
http://www.erols.com/rvenable

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From: "Igor J. Barani" <[email-masked]>
Date: Mon, 29 Jun 1998 17:00:09 -0400

Hello,

I am looking for a rapid way of creating MM2/MM3 input files.  Can anyone
recommend how I can do this by using either Chem3D or some other shareware
program?  Thank you.

Sincerely,
Igor Barani