nikhil damle wrote:
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"
pdb2gmx tries to cap termini of peptides automatically, but this isn't a
peptide. So look at pdb2gmx -h and choose the option that will allow you
to interactively choose that no terminal capping needs to take place.
Mark
------------------------------------------------------------------------
*From:* Mark Abraham <mark.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@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
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