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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 29 2021 - 10:00:03 PST
