I am trying to use trjconv to generate a new .xtc file in which all
frames have been aligned based on a subset of atoms (e.g. I have a
multi-domain protein and I want to align the trajectory to one of the
domains). Using a standard .ndx file only outputs the atoms
associated with the fitted domain. I was wondering if there is a
straightforward way to do what I describe without having to hack
trjconv?
Looking at the source for do_fit.c it looks like if I were to set the
mass of atoms that I didn't want to use in the alignment to zero,
then it might work, but I am generally trying to avoid having to
generate a tpr file since I'm coming from the pdb/psf world.
Any suggestions would be appreciated.
Josh
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Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/
~jadelman
Berkeley, CA 94720 USA jadel...@berkeley.edu
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