[gmx-users] compatibility of MOPAC charges with GROMACS ?

[Daniel Rigden]

Dear all

I'm trying to assemble a topology entry for S-nitrosocysteine.
Searching through the examples in the PDB revealed quite a spread of
bond lengths and angles - the N=O bond ranges from 1.2 to 1.47A, for
example.

To get more rigorously derived figures, and to calculate charges, I
thought of using MOPAC
http://www.openmopac.net/index.html
I imagine that the bond lengths and angles from MOPAC will be reliable.
My question is really how compatible the charges are with the GROMACS
topologies?  Would you have any qualms about mixing and matching?
Surely MOPAC's estimates must be better than human guesstimates or,
despite its general wonderful usefulness, PRODRG's estimates?  Are there
other programs for this?

Any thoughts welcome

Regards

Daniel

-- 
Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
School of Biological Sciences             FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.