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. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
