I see - in that case the best thing to do is to strip each incoming
trajectory to a common "core" of atoms. For example, if the first
trajectory has an extra 2 residues at the beginning, you might do
something like:
# Load traj1, strip first 2 residues
parm parm1.parm7
trajin traj1.nc
strip :1,2
createcrd MyCrd
run
# Load traj2 and append
parm parm2.parm7
trajin traj..nc parmindex 1
createcrd MyCrd
run
# Cluster
runanalysis crdset MyCrd <other options>
If you need to extract the non-stripped frames you can use the
resulting cluster number vs time file and filter out the frames you
need (using e.g. 'readdata', 'filter' etc).
Hope this helps,
-Dan
On Sun, Jun 7, 2020 at 7:43 PM Ranim Maaieh
<ranim.maaieh.mail.utoronto.ca> wrote:
>
> Hi Dan,
>
> The numbering of the residues was a bit different between them because I prepared them a bit differently.
>
> Ranim
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Tuesday, May 26, 2020 10:54 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] clustering parameter files
>
> Hi,
>
> I'm not sure I understand the issue. If they are the same structure
> the they should work with the same topology, right?
>
> -Dan
>
> On Mon, May 25, 2020 at 10:36 AM Ranim Maaieh
> <ranim.maaieh.mail.utoronto.ca> wrote:
> >
> > Hi all,
> >
> > Is it possible to use cpptraj to do combined clustering on simulations with different parameter files using parameter tagging? In this case, they are the same structure but the loops of the structure were initially modeled a bit differently therefore they have different starting structures. If not could I cluster using the same parameter file?
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 24 2020 - 06:00:10 PDT
