AMBER Archive (2004)

Subject: Re: AMBER: Problem with a single aminoacid as inhibitor

From: david.evans_at_ulsop.ac.uk
Date: Wed Nov 17 2004 - 06:55:58 CST

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

---- Message from Daniel Wetzler <danielwetzler_at_appleinfo.de> 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
>--------------------------------------------------------------------- 

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