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
Received on Tue May 27 2014 - 08:00:02 PDT
