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.
