[gmx-users] PYP chromophore force field

2011-04-20 Thread Ramachandran G
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.

Re: [gmx-users] PYP chromophore force field

2011-04-20 Thread Peter C. Lai
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

Re: [gmx-users] PYP chromophore force field

2011-04-20 Thread 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 ] OC +SG CA1 C +SG C +SG +CB [ dihedrals ] O C +SG+CB

Re: [gmx-users] PYP chromophore force field

2011-04-20 Thread Mark Abraham
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]