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 | =============================================================== -- 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
