On Thu, Jun 9, 2016 at 3:40 PM, Aishani Prem <aishaniprem.gmail.com> wrote:
> The command goes like:
> $AMBERHOME/bin/cpptraj -p pdb_vac.prmtop -i rmsd_cpptraj.trajin
> >cpptraj.log
>
>
you throw all the log output to cpptraj.log.
Hai
> On Thu, Jun 9, 2016 at 12:33 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Strange. How are you executing cpptraj (exact command on the command
> line)?
> >
> > Also, I recommend updating to AmberTools 16 if possible.
> >
> > -Dan
> >
> > On Thu, Jun 9, 2016 at 1:31 PM, Aishani Prem <aishaniprem.gmail.com>
> > wrote:
> > > It wont throw me an output file or an error, and the version I am using
> > is
> > > V15.00
> > >
> > > On Thu, Jun 9, 2016 at 12:17 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> > >
> > >> Can you please post your entire cpptraj output? Also, what version of
> > >> cpptraj are you using?
> > >>
> > >> -Dan
> > >>
> > >> On Thu, Jun 9, 2016 at 1:14 PM, Aishani Prem <aishaniprem.gmail.com>
> > >> wrote:
> > >> > Hi,
> > >> > I am trying to get the RMSD of the backbone atoms for a
> specific
> > >> set
> > >> > of residues in my simulations. My input file looks like:
> > >> > trajin pdb_nocut.mdcrd
> > >> > reference pdb_nocut.rst
> > >> > autoimage
> > >> > rms reference mass out pdb_backbone_nocut_cpptraj.rms .N,CA,C,O
> > :76-112
> > >> > time 0.1
> > >> >
> > >> > When I run this , I dont get any error but my output file is not
> > >> generated
> > >> > either. Am I doing anything wrong?
> > >> > --
> > >> > Thank You and Regards,
> > >> > Aishani Chittoor Prem
> > >> > _______________________________________________
> > >> > 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 307
> > >> Salt Lake City, UT 84112-5820
> > >> http://home.chpc.utah.edu/~cheatham/
> > >> (801) 587-9652
> > >> (801) 585-6208 (Fax)
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > >
> > > --
> > > Thank You and Regards,
> > > Aishani Chittoor Prem
> > > _______________________________________________
> > > 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 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thank You and Regards,
> Aishani Chittoor Prem
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jun 09 2016 - 13:00:04 PDT
