The combination of "clear trajin" and "run" worked perfectly, thanks.
On Tue, May 27, 2014 at 11:20 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You just need to pop a 'run' command after your first 'trajin' then
> 'clear trajin' so the first trajectory isn't used again, e.g.:
>
> parm sys1.parm7 [sys1_parm]
> reference sys1.rst7 parm [sys1_parm] [sys1_ref]
> trajin sys1.nc parm [sys1_parm]
> rmsd rmsd1 <mask> ref [sys1_ref] out rmsd.dat
> run
> clear trajin
>
> parm sys2.parm7 [sys2_parm]
> trajin sys2.nc parm [sys2_parm]
> rmsd rmsd2 <mask> ref [sys1_ref] out rmsd.dat
> run
>
> This should work, let me know if not. Actions are cleared whenever
> they are successfully used so you don't need to worry about the first
> 'rms' command being run twice.
>
> You can also get the same effect by loading the trajectories as
> COORDS/TRAJ data sets ('loadcrd'/'loadtraj') and using 'crdaction'.
>
> Hope this helps,
>
> -Dan
>
>
> On Tue, May 27, 2014 at 8:43 AM, Brian Radak <radak004.umn.edu> wrote:
> > I'd like to use cpptraj to calculate the RMSDs of several trajectories of
> > different lengths and slightly different topologies (differences in
> > protonation states and bound ions) with respect to the same reference
> > structure.
> >
> > Here's some pseudo commands assuming two trajectories of "sys1" and
> "sys2".
> > <mask> gives the exact same number of atoms for both systems.
> >
> > ==========
> > parm sys1.parm7 [sys1_parm]
> > reference sys1.rst7 parm [sys1_parm] [sys1_ref]
> > trajin sys1.nc parm [sys1_parm]
> >
> > rmsd rmsd1 <mask> ref [sys1_ref] out rmsd.dat
> >
> > parm sys2.parm7 [sys2_parm]
> > trajin sys2.nc parm [sys2_parm]
> >
> > rmsd rmsd2 <mask> ref [sys1_ref] out rmsd.dat
> > ==========
> >
> > This does give me two data sets (rmsd1 and rmsd2) in rmsd.dat, as
> > requested, but they include ALL of the frames loaded via trajin and both
> > data sets are thus identical. Of course I'd like them to be different so
> > that I can tell which rmsd values come from which trajectory/topology
> > (although I suppose I could just do this by counting the frames, that
> > sounds tedious and requires some kludgy scripting).
> >
> > Suggestions?
> > Brian
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > 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) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 27 2014 - 09:00:03 PDT
