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.
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
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 ]
OC +SG
CA1 C +SG
C +SG +CB
[ dihedrals ]
O C +SG+CB
On 4/21/2011 10:12 AM, Ramachandran G wrote:
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
That's your .rtp entry. What's in your [molecules]
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