Re: [gmx-users] Topology file for simulation of inorganic compounds
On 2012-08-13 21:39, Justin Lemkul wrote: On 8/13/12 1:49 PM, Deepak Ojha wrote: Dear All I want to do simulation of some ions like azide ion,thiocynate ion and other inorganic compounds in liquid water. I am not sure how to generate topology file for the same.How can I go about doing the same. Likely you will have to do it manually, which means you will have to understand Chapter 5 of the manual and the proper parameterization protocol for your molecules under the chosen force field. Some web servers exist for such purposes, depending on the force field you want to use. Otherwise consult the following page and be prepared for a significant time investment: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Hm, that page is slightly outdated. You want to google for antechamber / gaff /amber respectively charmm / cgenff -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Topology file for simulation of inorganic compounds
On 8/13/12 1:49 PM, Deepak Ojha wrote: Dear All I want to do simulation of some ions like azide ion,thiocynate ion and other inorganic compounds in liquid water. I am not sure how to generate topology file for the same.How can I go about doing the same. Likely you will have to do it manually, which means you will have to understand Chapter 5 of the manual and the proper parameterization protocol for your molecules under the chosen force field. Some web servers exist for such purposes, depending on the force field you want to use. Otherwise consult the following page and be prepared for a significant time investment: http://www.gromacs.org/Documentation/How-tos/Parameterization -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 * Only plain text messages are allowed! * 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] Topology file for simulation of inorganic compounds
Dear All I want to do simulation of some ions like azide ion,thiocynate ion and other inorganic compounds in liquid water. I am not sure how to generate topology file for the same.How can I go about doing the same. -- DeepaK Ojha School Of Chemistry "Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live" -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
