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

From: FyD <>
Date: Thu, 09 Jan 2014 21:28:41 +0100

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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Received on Thu Jan 09 2014 - 12:30:06 PST
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