Re: [AMBER] Can we perform combined clustering with multiple prmtop files and mdcrd files?

From: Kenneth Huang <>
Date: Fri, 29 Jan 2021 12:51:32 -0500


I think you want the tagging function in cpptraj so something like

parm traj1.prmtop [t1]
trajin 1 last 1 parm [t1]
parm traj2.prmtop [t2]
trajin 1 last parm [t2]

So each new trajectory is loaded with its respective topology, and then
have your RMS/imaging/clustering commands, etc.

Or since it's the same system, you could also just strip them out so they
have the same number of atoms, and just make a new prmtop for that by
something like

parm traj1.prmtp
parmstrip :WAT,Na+,Cl-
parmwrite out combined.prmtop



On Fri, Jan 29, 2021 at 9:37 AM Debarati DasGupta <> wrote:

> Hello,
> I want to perform clustering of 20 independent trajectories ( the protein
> backbone is same), the simulations are done in different cosolsvents.
> How I can I load in all the prmtops and trajectories in one combined run
> and cluster them?
> Many thanks
> Debarati
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Received on Fri Jan 29 2021 - 10:00:03 PST
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