[gmx-users] PYP chromophore force field
gtrama at gmail.com
Thu Apr 21 02:12:02 CEST 2011
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.
[ 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.
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
> 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
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