Re: [AMBER] To get resp charges of a modified central residue (not an integer).

From: Jason Swails <>
Date: Tue, 15 Jul 2014 09:02:00 -0700

On Tue, Jul 15, 2014 at 8:24 AM, Baptiste Legrand <>

> Dear all,
> I tried diverses strategies to get resp charges of an exotic amino acid
> (a dipeptide actually) and to incorporate it in a peptide sequence but
> without success (not an integer) . Can you give me your opinion, please?
> For example:
> First, I built a pdb of my modified residue (NH2-MOD-COOH) then I

If you want the charge of MOD to be an integer, you have to constrain the
net charge of the NH2 and COOH to be net neutral. If their charges are net
neutral, the charge of MOD will be an integer. The contrapositive is also
true -- if the charge of MOD is not an integer, then the net charge of NH2
and COOH is not neutral.

R.E.D. can include these intramolecular charge constraints (they have many
tutorials describing the process). However, I think they may suggest the
use of different caps (like the acetyl cap and n-methyl cap), since the
amine and carboxylate groups are fairly reactive and are susceptible to
proton transfers. The other caps I mentioned are not.

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 15 2014 - 09:30:02 PDT
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