Subject: summary of DMSO charmm parameters

From: wei <[email-masked]>
Date: Sun, 13 Apr 2003 10:55:37 -0400

Hi, all:

following are my original mail and the replies:

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ORIGINAL
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>Hi, guys:

>I want to do a simulation of a peptide in DMSO. Can anybody point me to 
>some paper about the parameters of DMSO which I can use? thanks a lot.
>

>best regards
>Wei Zhuang
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REPLY 1 FROM Scott Feller <[email-masked]>
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M.L. Strader and S.E. Feller, "A Flexible All-atom Model of 
Dimethylsulfoxide for Molecular Dynamics Simulations", J. Phys. Chem. A, 
106, 1074-1080 (2002).

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REPLY2 FROM Hannes Loeffler <[email-masked]>
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Strader and Feller, J. Phys. Chem. A 106 (2002), 1074

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REPLY3  FROM Jeff Nauss" <[email-masked]>
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You may look at:

Strader ML, Feller SE. 2002. A Flexible All-Atom Model of Dimethyl 
Sulfoxide for Molecular Dynamics Simulations. J Phys Chem A 106: 1074 
Mihailescu D, Smith JC. 1999. Molecular dynamics simulation of the cyclic 
decapeptide antibiotic, gramicidin S, in dimethyl sulfoxide solution. J 
Phys Chem B 103: 1586

Two different models.

Jeff
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REPLY4 FROM  
"C. Michael McCallum" <[email-masked]>
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Hi Wei,

Check out Krzysztof's site:

http://pekoe.chem.ukans.edu/~kuczera/Public/web/html/charmm/proc/ 
proc.html

It has a fairly detailed tutorial utilizing DMSO.

Cheers,

Mike

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REPLY 5 "Ya-Jun Zheng" <[email-masked]>
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The AMBER-type DMSO parameters used in the following paper could be adopted
in your CHARmm simulations:

A molecular dynamics and quantum mechanics analysis of the effect of DMSO
on enzyme structure and dynamics: substilisin,
 Zheng, Y. -J.; Ornstein, R. L.. J. Am. Chem. Soc. 1996, 118, 4175-4180.

Yajun