[gmx-users] using CHARMM force field for organic molecule
Dear , I want to use charmm force field to simulate the protein and ligand system. The protein can selcet charmm27 in gromacs, but i don't konw how to get the charmm force field for the ligand. could tell me a simple way to get the to Topology file for the organic molecule . thank you ! -- 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] using CHARMM force field for organic molecule
On 4/22/13 7:38 AM, aixintiankong wrote: Dear , I want to use charmm force field to simulate the protein and ligand system. The protein can selcet charmm27 in gromacs, but i don't konw how to get the charmm force field for the ligand. could tell me a simple way to get the to Topology file for the organic molecule . There are several options, all external to Gromacs: https://www.paramchem.org/ http://www.swissparam.ch/ -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] using CHARMM force field for organic molecule
a simple way is x2top Dr. Vitaly Chaban On Mon, Apr 22, 2013 at 1:38 PM, aixintiankong aixintiank...@126.comwrote: Dear , I want to use charmm force field to simulate the protein and ligand system. The protein can selcet charmm27 in gromacs, but i don't konw how to get the charmm force field for the ligand. could tell me a simple way to get the to Topology file for the organic molecule . thank you ! -- 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 -- 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] using CHARMM force field for organic molecule
On 04/22/2013 01:43 PM, Justin Lemkul wrote: There are several options, all external to Gromacs: https://www.paramchem.org/ http://www.swissparam.ch/ -Justin did paramchem support gromacs? As far as I know it only export in CHARMM format. Albert -- 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] using CHARMM force field for organic molecule
On 4/22/13 8:32 AM, Dr. Vitaly Chaban wrote: a simple way is x2top Using g_x2top implies that the charges and atom types that are to be assigned are already known. If the compound is not parameterized already, g_x2top is fairly useless in this case. -Justin On Mon, Apr 22, 2013 at 1:38 PM, aixintiankong aixintiank...@126.comwrote: Dear , I want to use charmm force field to simulate the protein and ligand system. The protein can selcet charmm27 in gromacs, but i don't konw how to get the charmm force field for the ligand. could tell me a simple way to get the to Topology file for the organic molecule . thank you ! -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] using CHARMM force field for organic molecule
On 4/22/13 9:50 AM, Albert wrote: On 04/22/2013 01:43 PM, Justin Lemkul wrote: There are several options, all external to Gromacs: https://www.paramchem.org/ http://www.swissparam.ch/ -Justin did paramchem support gromacs? As far as I know it only export in CHARMM format. If you have parameters (in whatever format), conversion into Gromacs format is fairly straightforward. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
