Re: [AMBER] distrbuting an excess charge

From: Jason Swails <>
Date: Mon, 12 Apr 2010 06:16:30 -0400

I would suggest trying to perform some kind of resp fit on a capped
version of this residue that restrains the net charge of the caps to
be 0, or something like that (and therefore all electrons on the
residue of interest are captured). R.E.D. is useful in this regard,
and there are numerous tutorials on their website to help with this
exact problem.

Good luck!

On Mon, Apr 12, 2010 at 1:50 AM, Homa Azizian <> wrote:
> Hi,
> I am new user of amber. I want to creat library file for carbamylated-lysin (as non-standard residue) wih total charge of -1. At the final stage, after I constructed it with xleap, I must omit two hydrogens: one from H-C=O and the other from H-N-H peptide bond, As the other standard residues don't have them. The residue's charge changes from -1 to -1.396250. So I must distribiute the 0.396250 excess charge to C and N. But I dont know how to add these chages (with which proportion) to C and N.
> Any suggestion would be appreciated.
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Apr 12 2010 - 03:30:04 PDT
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