Re: [AMBER] Modelling stereochemical molecule with "R" and "S" type.

From: Vijay Manickam Achari <>
Date: Fri, 10 Jan 2014 05:43:08 +0000 (GMT)

Thank you for the info sir.
I shall try this.

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,

On Friday, 10 January 2014, 4:48, FyD <> wrote:
Dear Vijay Manickam Achari,

A given force field library (with a given set of charge values) can be 
used for 2 enantiomers; however not for diastereoisomers.

You can convert an enantiomer into its image by transforming the x 
coordinates into -x.

regards, Francois

> I have modelled a glycolipid molecule with sugar and two 
> alkylchains. At the chain branching point there is a chiral center. 
> I have used antechamber & glycam  to generate a topology file for 
> hat molecule. 
> When I checked the modelcule with GAUSSVIEW, I notice it has "R" 
> type stereochemistry.  I used a tool called "invert" in the 
> GAUSSVIEW software to model a "S" type stereochemical molecule.
> Now I want to generate a topology for the "S" type molecule. 
> My question is can I use the same topology as I used for "R" type 
> molecule for this new molecule or else I need to generate start from 
>  scratch?

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