[gmx-users] Parametrization of Arsenic

David van der Spoel spoel at xray.bmc.uu.se
Sun Feb 17 11:50:40 CET 2013

On 2013-02-17 11:10, Kshatresh Dutta Dubey wrote:
> Dear all,
> I have to parametrize As(OH)3 for simulation using gromacs. I have already optimized the molecule using Gaussian and calculated ESP charge fitting. However, I have no idea to generate the .gro and corresponding topology file for this non-standard molecule. Can anyone suggest me tool that can parametrize the molecule according to gromacs library. I have already tried on Automated topology builder (ATB) server, PRODRG server and antechamber, but every time job failed to generate parameters and coordinate file. Using antechamber, however, I successfully generated corresponding .gro file, but molecule has absolutely different geometry from original one. I deeply appreciate any suggestion.
> Regards
> Kshatresh
Replace the As atom by P, and then feed it to antechamber (acpype) to 
make a topology and coordinate file. Then edit the topology to replace 
the P by As again, and modify the parameters such that the bond lengths 
and angles match the ones you get from QM. Are you sure this is a stable 
molecule by the way? I would expect it to loose at least one proton in 

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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