[gmx-users] PYP chromophore force field

[Ramachandran G]

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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