AMBER Archive (2006)

Subject: Re: AMBER: Charges of enantiomers for Amber8

From: lily ferreira (lily_1_mart_at_yahoo.fr)
Date: Thu Jan 26 2006 - 00:46:53 CST

  

> I saw that the results of RESP did not gave the
> mean values for 10 conformations, but charges for each conformation. My
> questions are:

First fitting is not averaging.
Yes we observed the same things, and we are working on this...

> 1. If I use 10 conformations for charges determinantion, after using RESP
> for
> the 10 conformations, do I have to take the mean value of the 10
> molecules or
> is there a specific command in resp that allows it to do that directly?

You could use R.E.D.-II http://www.u-picardie.fr/labo/lbpd/RED/ to calculate
RESP charges for your 10 conf. or for each conf. taken individually...

> 2. When I am working with enantiomers in Amber8, should we used the
> same
> charges for both enantiomers or have we to calculate the charges for
> (R)-enantiomers AND for (S)-enantiomers? (my molecules have only one
> chiral centre).

There were similar questions about this topic in the AMBER mailing list. Do a
google search in the AMBER mailing list using 'RESP charge' & 'enantiomers'.

Enantiomers (and diasteroisomers) are not differentiate in LEaP (if they do
present the same atom/residue names).

regards, Francois

    
Fitting is not averaging! But at the end of the RESP
calculations do we have to average the 10 charges?Because when we use LEaP,
we have only to work with one set of charges for the enantiomers! So, how
to procede after the calculation of the RESP charges of our 10
conformations?

Thank you very much

Lily

  

                
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