From: Mi Yang (
Date: Thu Oct 28 2021 - 08:35:40 CDT

Dear Natalia,
Thanks for your comments. We have slightly revised our script in the light
of your comments, which we were using for the Ligand-Protein complex. It
worked fine for us now. Please see the attached script in case, if anyone
else needs it.
One has to change the range of ligand atoms numbers.

On Thu, Oct 28, 2021 at 2:42 PM Natalia Ostrowska <> wrote:

> I made like three mistakes in these commands 😅 I was writing from my
> phone. You can email me for the correct version later, but this is
> definitely the kind of script you need
> On Thu, 28 Oct 2021, 13:33 Natalia Ostrowska, <>
> wrote:
>> Hi,
>> 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
>> How-to:
>> 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