[gmx-users] PYP Connection

[Taylor Kaplan]

Hi Rama,

   I was looking at the tdb files for the amber03 force field ( I didn't change anything, i just read with the cat command ), anyways I didn't see anything written in the tdb -n or -c terminal files. After reading the gromacs manual on topology files, it said that residue connection types and such are specified through the tdb file. I'm only guessing that since the chromophore isn't an amino acid that it may have a different connection deviating from the traditional -n or -c terminals. So I was wondering if the amber force field was using the .tdb files that comes standard with gromacs ,... which I'm pretty sure lacks the type of connection that pyp makes with the protein. So to fix this problem, do we need to make or modify the .tdb file for the chromophore, or is the .tdb file of no concern? 

Thanks,

Taylor

--- On Wed, 4/20/11, Ramachandran G <gtrama at gmail.com> wrote:

From: Ramachandran G <gtrama at gmail.com>
Subject: Re: [gmx-users] PYP chromophore force field
To: "Peter C. Lai" <pcl at uab.edu>
Cc: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Date: Wednesday, April 20, 2011, 5:12 PM


Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to the Sulphur(S) atom of the Cys-69 residue.
But I specified the covalent bond in my topology.

[ bonds]
 C   +SG

[ angles ]

      O    C   +SG   
     CA1   C   +SG   
      C  +SG   +CB  

[ dihedrals ]
      O     C  +SG    +CB
     CA1    C  +SG    +CB
     HA2   CA1   C   +SG
     CA2   CA1   C   +SG
      C   +SG  +CB   +CA

      C   +SG  +CB   +HB1
      C   +SG  +CB   +HB2

After doing pdb2gmx, i got the right structure. But the chromophore flies away after minimising. 


Thanks
Rama

On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai <pcl at uab.edu> wrote:

Isn't the chromophore supposed to be covalently bonded to the protein?

My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al

1994 and van Beeumen et al 1993: "This small 125-residue protein contains a

p-coumaric acid chromophore that is covalently bound to the protein backbone

via a thiol-ester cysteine linkage Cys-69"...



Maybe you forgot to specify a covalent bond in your topology...



On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:

> Hi gromacs users,

>      I am working on Photo active yellow protein.

>

>     Although i successfully build the force field and patched the chromophore to the protein.

> After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything?

> Please help.

> Rama

>

>



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Programmer/Analyst           | BEC 257

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