Thanks again That is it what I was asking. I have seen the topology files of t4-lysozyme with its ligand. It was provided by alchemistry.org tutorial. Can I change the topology accordingly. Another thing is the charge on the ligand molecule. How this will be handled in free energy calculations.
Waiting for your suggestion On Sat, Jan 7, 2017 at 10:35 AM, Amir Zeb <zebami...@gmail.com> wrote: > well > if you are confident of your simulation you may definitly go ahead with > this ff > otherwise you will have to change the ff for simulation too > i think this is not rational to simulate the system with one ff and then > change the ff for free energy calculations > > good luck > > On Jan 7, 2017 2:01 PM, "tasneem kausar" <tasneemkausa...@gmail.com> > wrote: > > > 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. > > > -- > 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.
