[gmx-users] Topology file for simulation of inorganic compounds

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 13 21:58:05 CEST 2012

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Hm, that page is slightly outdated.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

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