Re: AMBER: Problem with a single aminoacid as inhibitor

From: M. L. Dodson <>
Date: Wed, 17 Nov 2004 09:29:26 -0600

On Wednesday 17 November 2004 06:55 am, wrote:
> Hi,
> You don't describe exactly what system you're dealing with, so this
> may not be helpful, but
> there are parameters for N-terminal amino acids (in all_aminont.lib)
> So if you change the name of your protonated residue XXX in the pdb
> file to NXXX, it might recognise the NH3+ group. The basic problem is
> that leap has to match up atoms in residues in your pdb file to atoms
> in the residues defined in the .lib file, and if you input two extra
> hydrogens it will ignore them (maybe with a warning).
> Dave Evans
> London School of Pharmacy

Having been there, done that with a similar problem, I don't think
calling it NXXX will get the carboxylate right. IMO, what is
really needed is a new residue definition of the aa in the
zwitterionic protonation state. See the description on the web
site and the documentation for Antechamber. It can't be called the
same as any protonation state of a normal amino acid in the AMBER
FF descriptions or LEaP won't get the amine right (as already
observed) or the carboxylate right (try it and see, but I'm pretty
sure I'm correct on this). In any case, the distribution of
partial charges has to sum to 0 (unless it is asp, arg, etc) which
it won't if some form of a regular AMBER FF amino acid is used.
It would seem Antechamber is your friend.

Bud Dodson

> ---- Message from Daniel Wetzler <> at
> 2004-11-17 12:59:12 ------
> >Dear Amber-users,
> >
> >I have a problem with a single aminoacid which acts like a inhibitor
> for
> >a enzyme I'm dealing with.
> >My problem is, that this aminoacid should be fully protonated
> (NH3-group).
> >Regardless how I write this structure into my pdb-files (in its own
> >chain, as HETATM
> >a.s.o) xleap seems to handle it like a part of my structure and
> >protonates my N only with one H.
> >
> >If I protonate my structure with the protonate command I get the
> right
> >structure with NH3
> >but after using xleap to write the .top / .crd files I get the
> >deprotonated form again.
> >
> >Does anyone know how to change that behaviour ?
> >
> >Hope anyone can help.
> >
> >Best wishes,
> >
> >Daniel

M. L. Dodson                      
409-772-2178                                FAX: 409-747-8608
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Received on Wed Nov 17 2004 - 15:53:00 PST
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