Take a look at this publication with detailed information on how
atom-centered charges are derived in GLYCAM.
Kirschner et al. at
http://www3.interscience.wiley.com/cgi-bin/abstract/116311717/ABSTRACT
Good luck,
Austin-
> Quoting nag raj <nagaraju_chem.yahoo.co.in>:
>
>> My system consist of CH3 group in
>> place of primary and secondary hydroxyl hydrogen atom
>> of alpha-D-Glucose (Unit name is 4GA in glycam04 force
>> field of Amber8.0. Primary and secondary hydroxyl
>> hydrogen atoms in 4GA are replaced by CH3 group). As
>> per the example given in tutorial
>> http://amber.scripps.edu/antechamber/efz.html, I
>> calculated the RESP charges to with and without adding
>> CH3 group to 4GA unit. The charges of 4GA unit without
>> adding CH3 group do not match with 4GA unit of
>> glycam04.
>>
>> My question is:
>> How to calculate the charges to a system consist of
>> CH3 group in place of primary and secondary hydroxyl
>> hydrogen atom of alpha-D-Glucose.
>
> You could look at
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14
> and in particular the Scheme 5
> And apply what is done on the anomeric carbon to the positions you are
> interested in.
>
> regards, Francois
>
>
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Austin B. Yongye
Complex Carbohydrate Research Center,
University of Georgia,
315 Riverbend Road,
Athens, GA 30602.
Phone: 706 542 0263
"...then, we learn better in a free spirit of curiosity, than under fear
and compulsion..." -St. Augustine of Hippo
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Received on Sun Nov 11 2007 - 06:07:08 PST
