AMBER Archive (2006)

Subject: Re: AMBER: RESP charge fitting problems with capping group

From: FyD (
Date: Thu Jun 22 2006 - 13:51:13 CDT

Quoting hayden <>:

> My problem is that, even when I allow all the atoms to vary (i.e. set there
> values to 0 in second column), the restraints do not make the selected
> charges sum to 0. Why is that? And how can I get my capping groups to sum to
> zero so that when I cleave them I don't adversely affect the charge of the
> main saccharide unit?

I think you will find the answer there:

I would 1st run the job without intramolecular charge constraint and then with
intramolecular charge constraints. Then, compare the two RRMS values of the 2
jobs. Does the RRMS increase a lot by adding this/these intramolecular charge
constraint(s) ? If yes, this means that your choice of intramolecular charge
constraint/groupement is wrong.

regards, Francois

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