Dear Amber users,
I am very thankful to Francois , Karl, and Austin B. Yongye for their valuable suggestion to my query.
with best regards,
Nagaraja Mulpuri.
FyD <fyd.q4md-forcefieldtools.org> wrote:
Quoting nag raj :
> 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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Received on Sun Nov 11 2007 - 06:07:18 PST
