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

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

Hi,

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

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

Best,

Kenneth




On Fri, Jan 29, 2021 at 9:37 AM Debarati DasGupta <
debarati_dasgupta.hotmail.com> 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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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Fri Jan 29 2021 - 10:00:03 PST
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