Thank You that works!!!
On Thu, Nov 5, 2015 at 2:11 PM, V. Kumar <vin.vasanth.gmail.com> wrote:
> Hi
>
> this is another way to obtain rmsd using cpptraj.
>
> create a input file "rmsd_cpptraj.trajin"
> =========================================
>
> trajin monA_gb_md1_nocut.mdcrd
> reference monA_gb_md1_nocut.rst
> autoimage
> rms reference mass out monA_gb_md1_nocut_cpptraj.rms time 0.1
>
>
> command
> $AMBERHOME/bin/cpptraj -p monA_vac.prmtop -i rmsd_cpptraj.trajin >
> cpptraj.log
>
> On 5 November 2015 at 22:45, Aishani Prem <aishaniprem.gmail.com> wrote:
>
> > Hello,
> > I have been working on the amber B1 tutorial. When I use the
> cpptraj
> > command to generate the rmsd file I get :-
> > CPPTRAJ: Trajectory Analysis. V15.00
> > ___ ___ ___ ___
> > | \/ | \/ | \/ |
> > _|_/\_|_/\_|_/\_|_
> >
> > | Date/time: 11/05/15 13:29:39
> > | Available memory: 13178.9 MB
> >
> > Reading 'monA_vac.prmtop' as Amber Topology
> > TIME: Total execution time: 0.0263 seconds.
> >
> > But my rmsd is not generated. Can anyone tell me what is the problem.
> > My input file is :
> > trajin monA_gb_md1_nocut.mdcrd
> > rms first mass out monA_gb_md1_nocut.rms time 0.1
> > and my command is
> > $AMBERHOME/bin/cpptraj -p monA_vac.prmtop -i monA_gb_md1_nocut.calc_rms
> > I checked the mdcrd and prmtop files and they seem fine.
> > --
> > Thank You and Regards,
> > Aishani Chittoor Prem
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Thank You and Regards,
Aishani Chittoor Prem
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Received on Thu Nov 05 2015 - 14:30:05 PST
