Dear GMX users I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, respectively. While, I calculated binding energy before for many other complexes without any phosphate groups using OPLS all atom force field and pdie = 2 and obtained minus energy. But this time , I dont know why I got positive binding energy? Is it because of charmm36 all atom force field , the phosphate groups or it is needed to be energy minimized under more restriction situations? I am checking different factors to understand its reason, so I wanted to know , would it be ok if I energy minimize the complex with more restriction situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? I think the positive binding energy might be because of the complex didnt minimized well. however I checked the em.log file and saw it was minimized well:
Steepest Descents converged to Fmax < 1000 in 241 steps Potential Energy = -6.5047744e+05 Maximum force = 9.8285083e+02 on atom 3335 Norm of force = 3.6905827e+01 Is there anyone can advice me in energy minimization with emtol 800? Thank in advanceFarial -- 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.
