> 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?
What it comes back to is how the forcefield you are using is constructed. It will have been done using a particular procedure for generating the partial charges, L-J interactions, bonding etc to fit some particular parameters. If you use a different procedure to generate yours and try to mix it with the forcefield, then there is an extremely good chance you will get out garbage. So what you really need to do, once you have worked out which forcfield you are going to use, go back to the documentation / papers for that particular forcefield, see how they generated the parameters, then use that same procedure for the new parameters / molecules you want to generated. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ 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