[gmx-users] simulation of protein in presence of ATP

nikhil damle pdnikhil at yahoo.co.in
Tue Jun 23 08:44:19 CEST 2009

    We can use max 4 coloumns for naming atoms. But .rtp file has 5 coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now the error is "atom N not found in residue 1ATP while combining tdb and rtp"

From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, 23 June, 2009 11:16:26 AM
Subject: Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote:
> Hi,
>    Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I converted HETATM tag to ATOM tag. Still same error msg. Please find ATP.pdb file attached herewith.

You've broken the PDB format, which encodes the information in fixed-column style. See http://www.wwpdb.org/documentation/format32/v3.2.html

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