The biotin-streptavidin interaction is on the order of -75 kJ/mol, so a binding free energy of -300 kJ/mol (dissociation constant of 10^-52 M) means something is fundamentally wrong - start by taking a hard look at your protocol, as convergence problems wouldn't account for that kind of deviation.
________________________________ From: mohsen ramezanpour <ramezanpour.moh...@gmail.com> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wed, 29 December, 2010 20:36:59 Subject: [gmx-users] Free energy Dear All I estimated protein-ligand free energy about -300 kj Is it logical?I think it is wrong.what do you think? what is the range of correct value for a typical protein-ligand? protein=660 residue ligand=25 atom water=4670 Na=118 Cl=120 thanks in advance -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
