Re: Post processing NAMD trajectory

From: Josh Vermaas (
Date: Sun Sep 13 2020 - 15:56:12 CDT

Hi Dimuthu,

Sure! In VMD, you can change resids at will, or if you choose to select
based on residues instead of resids, you'll likely find the numbering
already matches what you want. The RMSD trajectory tool inherits its
biases from VMD selections in general. What I always tell folks is to
take the selection text in the upper left hand corner (the default is
"protein"), and see if the selection matches what you'd like it to
match. The whole protein will be both monomers, but if you'd like to
only look at one monomer, something like "fragment 0" or "segname PA"
will probably be the correct selections.


On 9/13/20 12:08 PM, Kodituwakku,Dimuthu Nirmani wrote:
> Hi all,
> I want to renumber residues of my trajectory sequentially. Currently,
> I have numbered my 2 monomers of my dimer starting from 1-587. Is
> there a way to number residues from 1-1174 in my trajectory?
> Also does using the VMD RMSD trajectory tool to calculate RMSD for the
> entire protein get affected by having residues numbered from 1-587 for
> the 2 monomers?
> Thank you,
> Best,
> Dimuthu

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