AMBER Archive (2006)

Subject: Re: AMBER: Charges of enantiomers for Amber8

From: FyD (
Date: Wed Jan 25 2006 - 03:38:36 CST

Quoting lily ferreira <>:

> 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 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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to