Dear GMX users i want to compare binding free energy between experimental and MD computations In experimental methods, we assumed that all atoms of a protein that binding to ligand, butin MD simulations, we just assume the sections of subdomain(s) that binds to ligand
Is this way correct to comparing the binding free energy have got from MD with experimental analysis? or in MD simulations, we must simulate all of subdomains in a protein whatever bind to a ligand or not? finally, suppose that there are for example 2 molecules of a ligand in a pdb file of a protein (for instance in pdb:2i30 there are 2 molecules of SAL we must suppose all of two molecules in pdb file or once, simulate protein with ligand1 (SAL1) and after that simulate with ligand 2 (SAL 2)? Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.