[gmx-users] PYP chromophore force field
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 listgmx-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
Re: [gmx-users] PYP chromophore force field
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 listgmx-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 listgmx-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
Re: [gmx-users] PYP chromophore force field
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 CA1C +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 listgmx-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 listgmx-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
Re: [gmx-users] PYP chromophore force field
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] section of your topology? Mark [ angles ] OC +SG CA1 C +SG C +SG +CB [ dihedrals ] O C +SG+CB CA1C +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 mailto: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 mailto: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 mailto: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 mailto:p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 tel:%28205%29%20690-0808 | === -- gmx-users mailing listgmx-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
