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 > > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > =============================================================== > 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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