Re: [AMBER] TMD setup

From: Simon Becker <>
Date: Mon, 06 Aug 2012 11:15:29 +0200

Hi Manish,

First you have to be absolutely cetain that the number of atoms in the
target and reference protein are identical. Also you have to add the
same number of couter-ions to both systems.

As for the waters, the official protocol is to play a bit with the
box-boundary values, until leap adds the correct number of waters. This
never worked for me however. I added to many waters to the reference
system and deletetd the remaining waters by editing the inpcrd file of
the reference system. Remember to adjust the number of total atoms in
the second line of this file.

This worked for me, and the resulting trajectory looked good.


On 06.08.2012 10:46, Manish Datt wrote:
> Hi All,
> I am trying to study conformational transition in a protein using TMD
> with amber10. I have prepared the two systems (reference and target)
> in explicit solvent in leap using the command:
> solvateOct unit TIP3PBOX 10
> Although the number of atoms in protein in the two systems are same
> but the total number of atoms are different because of different
> conformations of the protein and hence different number of water
> molecules in the box. While running the MD I specified target under
> the -ref flag. This gives an error
> FATAL: NATOM mismatch in constraint coord and topology files
> Could you please suggest how can I prepare the two system with equal
> number of atoms so that same topology file can be used for both
> systems.
> Thanks in advance,
> Manish
> _______________________________________________
> AMBER mailing list

Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647 Universitaet Konstanz
D-78457 Konstanz
Tel: 0049 7531 882900, Fax: 3183
AMBER mailing list
Received on Mon Aug 06 2012 - 02:30:03 PDT
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