I am using ptraj and Amber 11
*Best Regards,
Esam
*
On Wed, Oct 17, 2012 at 10:09 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Are you using ptraj or cpptraj? Also, what version of AmberTools do you
> ahve?
>
> -Dan
>
> On Wed, Oct 17, 2012 at 1:49 PM, Esam Tolba <eatolba.gmail.com> wrote:
> > Thanks for the note
> > I am using the this command for clustering
> > cluster out ***** representative pdb average pdb averagelinkage clusters
> 5
> > rms
> > I got as output three files for each cluster but the average and the
> > represintative files are empty and there is no error in the output file
> > *Best Regards,
> > Esam *
> >
> >
> > On Wed, Oct 17, 2012 at 3:26 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
> >
> >> On Wed, Oct 17, 2012, Esam Tolba wrote:
> >>
> >> > > See the 'cluster' command for ptraj or cpptraj. Note that currently
> >> > > ptraj clustering has far more options than cpptraj. Refer to the
> >> > > AmberTools manual for more details.
> >>
> >> > How to use the 'cluster' command?
> >> > and what would be the output files?
> >>
> >> We expect users to invest a fair amount of effort before asking people
> on
> >> the
> >> list to spend their time in replies. People are willing to help for
> >> reports
> >> like "I read Section xxx of the manual, but I don't understand this
> >> sentence...", or "I tried the following calculation, but I got a strange
> >> result....". [Even better is with the addition: "I searched the Amber
> mail
> >> archives and Googled the error message, but could not find the help I
> >> needed."]
> >>
> >> Just asking people on the list to tell you what is already in the
> Reference
> >> Manual is not a good use of anyone's time.
> >>
> >> ...dac
> >>
> >>
> >> _______________________________________________
> >> 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, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> 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 Oct 18 2012 - 01:00:03 PDT
