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

[Mark Abraham]

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.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
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