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

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


Hi,
 
    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

Mark
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



      Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090623/b7e579a5/attachment.html>


More information about the gromacs.org_gmx-users mailing list