The default output from ptraj (I forget the keyword) is almost the same as
what cpptraj 'info' prints out.
However, I agree with Hai that you should use cpptraj for a few reasons.
The principal one here is that 'cluster' in ptraj doesn't actually support
the 'nofit' keyword. In fact, ptraj will silently ignore any keyword it
doesn't understand, so in this case you're probably not getting the
behavior you expect.
Also, ptraj is no longer being actively developed. With a few exceptions,
input for cpptraj is the same as it was for ptraj (see the manual for full
details) and clustering in cpptraj is faster, so you should use cpptraj
unless you're using one of the clustering algorithms not supported by
cpptraj.
-Dan
On Thu, Dec 15, 2016 at 4:54 AM Mary Varughese <maryvj1985.gmail.com> wrote:
> Hi,
>
>
> Is there any command corresponding to 'info' in ptraj ?
>
> I am more familiarized with ptraj than cpptraj.
>
>
> Thanking you
>
> mary
>
> On 12/15/16, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> > 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
> >> >>
> >> >
> >>
> >> _______________________________________________
> >> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 15 2016 - 08:00:03 PST
