Re: [gmx-users] g_mmpbsa positive binding energy
Hi, MM/PBSA method has several limitations (discussed in several publications) and therefore, you may be getting positive energy values from these limitations. You may get a negative binding energy after further increasing the dielectric constant, however, interpretation of this value would be very difficult. g_mmpbsa calculates binding Enthalpy. It can be used to compare binding of several small ligands with same receptor protein because one may assume that entropy change is almost similar or negligible in all complexes. In case of large molecules binding, binding comparison s are highly unreliable as entropy cannot be neglected . Because of these reasons, I would not use MM/PBSA method for protein-protein complex. Regards, Rajendra -- 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.
[gmx-users] g_mmpbsa positive binding energy
Dear Gromacs Users I am trying to calculate binding energy of protein-ligand and protein-receptor complex using g_mmpbsa. I have run simulation of 10 ns and snapshot was generated at every 1 ps. Initial 2ns was not taken. g_mmpbsa was run for the rest of the frames. The command line was given as: g_mmpbsa -f protein.xtc -s protein.tpr -n protein.ndx -dt 200 -b 2000 -e 1 -pdie 2 protein.ndx is index file of protein-ligand and protein-receptor. The binding energy with dielectric 2 comes out positive. When I have increased the dielectric, binding energy is still positive. at dielectric 2 binding energy was 1028.010 kJ/mole at dielectric 4 binding energy was 428.010 kJ/mole at dielectric 8 binding energy was 128.015 kJ/mole I have calculated the charge on the ligand and receptor using pdb2gmx. The charge on the ligand protein is -12 and that of receptor protein is -5. How will I get the negative binding energy? Any suggestion resolving this issue will be appreciated. Thanks in Advance -- 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.
