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Hm, that page is slightly outdated.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.se http://folding.bmc.uu.se
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