Thanks Amir Zeb for your reply I have read in literature about the FEPsetup to parametrize the complex file (protein+drug) for simulation. This setup builds files based on amber. Since I have previously used 54a7ff to simulate the protein and drug and topology files were generated from ATB in gromos54a7 format. Since I didn't find free energy calculation of protein and ligand with this force field. Thats why I was confused to proceed further using the same.
On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar <tasneemkausa...@gmail.com> wrote: > mm/pbsa calculates binding energy. I have used that. > > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebami...@gmail.com> wrote: > >> hello >> you may use mm/pbsa compiled with gromacs to calculate free energy >> all the best >> >> On Jan 7, 2017 1:27 PM, "tasneem kausar" <tasneemkausa...@gmail.com> >> wrote: >> >> > Dear gromacs users >> > >> > It is first time I am trying to perform free energy calculation of >> protein >> > and drug complex. I am following Justin' s tutorial of mehtane in water. >> > That calculation are performed on a neutral system. If the ligand >> molecule >> > has charge what are the provisions that could be taken into account. >> > I have performed my MD simulation using force field gromos54a7. And Now >> I >> > am trying to go onward using free energy calculations. Since the free >> > energy calculations are performed on ambed99ldn, opls and charmm force >> > fields (as I know from the articles). Is it okay to use gromos54a7 ff >> for >> > free energy calculations. >> > >> > Kindly tell me >> > >> > 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. >> > >> -- >> 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. >> > > -- 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.