Thanks a lot Bratin for your help. It worked and I was able to get the RMSD values. However, there is no option to change the reference frame (from the input trajectory) for the RMSD calculation.
As a workaround, I was thinking about extracting the different frames of the ligand as separate .gro files but couldn't figure out how to do that easily. Can this be achieved using "trjconv" but without supplying multiple text files for the frame index values? Please let me know. On Wed, Feb 19, 2020 at 3:48 PM Bratin Kumar Das < [email protected]> wrote: > Hi, > You can calculate the rmsd by passing the index file of the ligand... > gmx rms -h > > On Wed 19 Feb, 2020, 7:41 PM Peter Mawanga, <[email protected] > > > wrote: > > > Hello everyone > > > > After fitting the protein-ligand system to the starting conformation, I > > would like to extract the RMSD information for the ligand only but cannot > > find such an option for a selective output. > > > > Please let me know if this can be achieved with the gmx tool, I couldn't > > find such an option with both the "rms" and "rmsd" commands. > > > > -- > > Thanks > > 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 [email protected]. > > > -- > 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 [email protected]. > -- 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 [email protected].
