The file written by 'out' will contain the cluster number for each frame.
In addition, the file written by 'info' will contain parseable text
representations of each cluster.
-Dan
On Wed, Dec 14, 2016 at 5:34 AM Mary Varughese <maryvj1985.gmail.com> wrote:
> Sir,
>
> I tried clustering in ptraj and it worked ok.
>
> When i tried to do mmpbsa.pl on the trajectory generated; snapshots
> are generating but on performing pbsa and nmode calculations, pbsa
> finishes giving huge negative values (7 or 9 digits) and nmode fails
> to run. Problems on missing bonds errors are also in the log file.
>
> Is there any other way to know which frames are included in each
> cluster (i could create snaphots if i know the frame numbers) or
> generate proper trajectory (manual says trajectory generated is in
> amber format by default).?
>
>
> Thanking you
>
> mary
>
>
> On 12/7/16, Mary Varughese <maryvj1985.gmail.com> wrote:
> > Ok.
> >
> > Thank you sir
> > I wil try this.
> >
> > On Wed, Dec 7, 2016 at 1:39 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> This is almost right, but what you want to do is RMS-fit the DNA
> >> _before_ you cluster, then cluster on your ligand using 'nofit'. So
> >> something like:
> >>
> >> parm myparm.parm7
> >> trajin mytraj.nc
> >> rms first <DNA backbone mask>
> >> cluster <ligand mask> nofit ...
> >>
> >> Hope this helps,
> >>
> >> -Dan
> >>
> >> On Thu, Dec 1, 2016 at 5:43 AM, Mary Varughese <maryvj1985.gmail.com>
> >> wrote:
> >> > Sir
> >> >
> >> > Thank you very much.
> >> >
> >> > This is a sample given in amber tutorial
> >> >
> >> > trajin traj.1.gz
> >> > trajin traj.2.gz
> >> > cluster out testcluster representative pdb average pdb averagelinkage
> >> > clusters 5 rms .CA
> >> >
> >> > Is the mask part you mentioned "rms .CA" ?
> >> >
> >> > Are you familiar with mmtsb (i always use mmtsb as learned from amber
> >> > tutorial) ? And do you know any keyword related to this?
> >> >
> >> > thanking you
> >> >
> >> > On Thu, Dec 1, 2016 at 3:56 PM, Achim Sandmann <
> >> > Achim.Sandmann.chemie.stud.uni-erlangen.de> wrote:
> >> >
> >> >> Hello Mary Varughese,
> >> >>
> >> >>
> >> >> So far as I understood, you want to take the ligand position with
> >> >> respect to the DNA (as well as the ligand conformation itself) into
> >> >> consideration.
> >> >>
> >> >> I think the easiest way to do this is to do a RMSD calculation with
> >> >> the
> >> >> DNA backbone mask first. This will align the structures. As a second
> >> >> step (within the same praj/cpptraj call) you can use the cluster
> >> >> command
> >> >> with the mask of the ligand and the 'nofit' flag.
> >> >>
> >> >>
> >> >> with kind regards,
> >> >>
> >> >> Achim Sandmann
> >> >>
> >> >>
> >> >> Am 01.12.2016 um 08:26 schrieb Mary Varughese:
> >> >> > Sir
> >> >> >
> >> >> > I have a DNA ligand system. After aligning all the structures with
> >> >> respect
> >> >> > to DNA backbone i want to cluster on the basis of ligand
> >> conformation. Is
> >> >> > there any way to specify that aspect in mmtsb or ptraj cluster.
> >> >> >
> >> >> > Thanking you
> >> >> >
> >> >> >
> >> >> > mary varughese
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe
> >> Laboratory of Computational Biology
> >> National Institutes of Health, NHLBI
> >> 5635 Fishers Ln, Rm T900
> >> Rockville MD, 20852
> >> https://www.lobos.nih.gov/lcb
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
>
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Received on Wed Dec 14 2016 - 11:00:05 PST
