Dear Rui, The atomic charges (and other FF properties) should match as closely as possible to the way the FF was developed. In AMBER, these were derived by fitting to a QM calculations IIRC, and in OPLS and CHARMM they're usually close to what you'd get from quantum chemistry with a medium basis set (the basis set it should be mentioned in the literature you read).
To get the atomic charges from a QM calculation, you should calculate the wave function of the molecule using a reasonable basis set (and usually after optimising the structure, to get you into a minimum). You can now calculate the average number of electrons associated with each atom and get a partial charge, but the results will have a strong dependence on the geometry of your system. Another option is to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential. This method is less sensitive to small changes in the geometry of the molecule, and is probably what you refer to. Ran. -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ 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
