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

[nikhil damle]

Hi

Thanks a lot for help. I could run the EM with ATP in its right place. But position restrained dynamics gives warnings saying that some angles are rotated beyond 30 deg. So when i directly went for MD run it is running fine. What dis-advantages i have of not performing position restrained dynamics on my ATP-receptor complex system ?

Regards,
Nikhil




________________________________
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 12:35:12 PM
Subject: Re: [gmx-users] simulation of protein in presence of ATP

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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