[gmx-users] Re: oplsaa parametrization

Alan alanwilter at gmail.com
Tue May 26 09:34:03 CEST 2009

Dear Rosa, here goes my little contribution to try to help you:
For me, no doubt that antechamber is the best tool for getting the
topological information about small molecules (pls, read the wikis in ACPYPI
pages to know more).

The module to generate OPLS/AA is still experimental but if you take
information from MKTOP (which I intend to add to ACPYPI eventually) then you
can get something good enough, specially if you do your homework and read
the papers related to this matter.


Subject: [gmx-users] oplsaa parametrization
> Dear Users
> I m trying to simulate a structure (not a protein) which is not
> parametrized in oplsaa FF. I created the structure using PRODRG and
> included the results of *.itp from PRODRG to ffoplsaa.rtp file and tried
> to use available oplss_xxx for my atom type near to those ones already
> exists in *.atp. I also optimized my structure at RHF/6-31G* level and
> calculated the charge using resp. Then updated ffoplsaa.rtp using this
> calculated charge. By refering to the mailing list it seems that I need
> to modify bn.itp and nob.itp file as well (?!). I m just wonder if
> anybody use PRODRG how he/she parametrized FF. As I m new in GROMACS and
> any tutorial or procedure to follow will help me so much. Thank you in
> advance for any ideas or comments.
> Also when I use pdb2gmx, I have this warning; all CONECT records are
> ignored. However when I proceed with energy minization in vacuum the
> program doesnt complain and it can produce *.tpr file.
> Regards
> Rosa
> --
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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