VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Oct 28 2021 - 06:28:27 CDT

Is the reviewer asking for RMSD/RMSF of ligand from the complex you have
simulated? or just the ligand independently?

These two are separate things.
If the ligand flexibility is under question then you probably have to run a
new MD simulation of just the ligand alone.

If you want to calculate the RMSD/RMSF of the ligand while it is bound to
the protein, you can load the complex, select the ligand and run the
RMSD/RMSF calculation only on this.
This is what you are trying (I think), but unless you mention "what" the
error is no one will be able to help you.

Your explanation is also a little confusing.

I wrote UNK and/or LIG ETC. as per psf file

You have the PSF - you should know EXACTLY what to select for. Shouldn't
you?

Another way is to use the catdcd plugin to extract the ligand from the DCD
of the complex and write out another DCD which contains JUST the ligand
(see plugin and examples here:
https://www.ks.uiuc.edu/Development/MDTools/catdcd/) and then use the same
thing you used before (not sure what/how you did before) to calculate on
this new DCD - only now you can use the keyword "all" as the only thing in
your DCD would be the ligand.

Regards,
Ashar

On Thu, Oct 28, 2021 at 6:21 PM Mi Yang <drmiyang2019_at_gmail.com> wrote:

> Dear Colleagues,
> We have performed MD for RMSD and RMSF calculation of Ligand-protein
> complex using NAMD/VMD. Now, one reviewer is insisting us to also calculate
> RMSD and RMSF of Ligand only.
> Is there a way to extract RMSD and RMSF of Ligand only from a .dcd file or
> through a separate MD?
> I have tried RSMD calculator of VMD after opening the psf,pdb and dcd file
> but "atom selection" is giving error. I wrote UNK and/or LIG ETC. as per
> psf file but none worked..
>
> Many thanks in advance1
> DR.SHABBIR
>