[gmx-users] Selective RMSD calculation

[Bratin Kumar Das]

Hi
   You have said correctly...you can use trjconv for that..

On Thu 20 Feb, 2020, 4:30 PM Peter Mawanga, <peter.mawanga.lagos at 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.bratin at 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.lagos at 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
> > > --
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>
> --
> Cheers
> Peter
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