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
solution.
--
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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