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 <gtr...@gmail.com> wrote:
From: Ramachandran G <gtr...@gmail.com>
Subject: Re: [gmx-users] PYP chromophore force field
To: "Peter C. Lai" <p...@uab.edu>
Cc: "gmx-users@gromacs.org" <gmx-users@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 <p...@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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--
===============================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | BEC 257
Genetics, Div. of Research | 1150 10th Avenue South
p...@uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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