[gmx-users] Parametrization of Arsenic

Kshatresh Dutta Dubey kshatresh at ymail.com
Sun Feb 17 11:10:12 CET 2013

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.


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