Hi.. You have to specify energy groups in .mdp option..then rerun the simulation..and analyse with gmx energy command
On Mon 17 Feb, 2020, 5:52 PM Александр Лашков, <alashko...@gmail.com> wrote: > You can rebuild index file using gmx make_ndx gromacs util. > Alex > > пн, 17 февр. 2020 г. в 15:19, Peter Mawanga <peter.mawanga.la...@gmail.com > >: > > > Hello everyone > > > > I used the CHARMM-GUI Membrane Builder to build a bilayer around my > > protein-ligand complex. > > > > However, unfortunately the ligand was not mentioned separately in the > index > > (.ndx) file although it was mentioned in the topology (.top) file. Hence > I > > am not able to calculate the energy between the protein and ligand using > > the energy (.edr) file. > > > > Please let me know if there is any workaround for this. It would be > > difficult to repeat the simulations again. > > > > > > -- > > Cheers > > Peter > > -- > > 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.