[gmx-users] sulfate in topology file with oplsaa forcefield

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 7 00:29:26 CEST 2010

you zou wrote:
> Dear users,
> I have to complete my topology file and there is sulfate(SO4(-2)) in pdb 
> file. But I don't know how can I complete this file with oplsaa 
> forcefield. I can't find so4 in ffopls.tpr file. I would really 
> appropriate if you could do this for me.

I truly doubt anyone on this list is going to do your work for you. 
Parameterization is an advanced topic, and it could take months to develop 
appropriate parameters for new species.  Do your homework - understand the 
intrinsics of the force field you've chosen, read literature pertaining to how 
others have employed this force field (or perhaps developed the parameters you 
want), and set about the difficult task you've given yourself.


> thank you
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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