[gmx-users] Selective RMSD calculation

[Peter Mawanga]

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