Hi You have said correctly...you can use trjconv for that.. On Thu 20 Feb, 2020, 4:30 PM Peter Mawanga, <peter.mawanga.la...@gmail.com> wrote:
> 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 < > 177cy500.bra...@nitk.edu.in> 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, < > peter.mawanga.la...@gmail.com > > > > > 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 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. > > > > > -- > 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.
