The command goes like:
$AMBERHOME/bin/cpptraj -p pdb_vac.prmtop -i rmsd_cpptraj.trajin
>cpptraj.log
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
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Received on Thu Jun 09 2016 - 13:00:03 PDT
