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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Nov 05 2015 - 14:30:02 PST
