Re: RMSD and RMSF of ligand Only

From: Natalia Ostrowska (
Date: Thu Oct 28 2021 - 06:42:29 CDT

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, <>

> 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

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