Re: RMSD and RMSF of ligand Only

From: Natalia Ostrowska (
Date: Thu Oct 28 2021 - 06:33:24 CDT

You don't have to run any additional simulations etc
Let me introduce you to the glorious tk console :P :P
let's say you have 1000 frames. type something like
set n 0
set ref atomselect ["your ligand" frame 0]
for {set i 0} {$i<1001} {incr i} {
   set conf [atomselect top "your ligand" frame $i]
   puts "$i [measure rmsd $ref $conf]" }

"Your ligand" will be something like "resid X" or "chain Y and resid 23 to
39", have a look at your pdb file, and find how is the ligand called etc
and look for the atomselect commands in the tutorial. I think pdb + dcd
files will work, you don't need PSF for this particular case


On Thu, 28 Oct 2021, 11:50 Mi Yang, <> 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

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