From: Mi Yang (
Date: Thu Oct 28 2021 - 04:48:37 CDT

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