From: Stefan Franzen (Stefan_Franzen_at_ncsu.edu)
Date: Mon May 03 2010 - 17:42:18 CDT
I have tried to apply the directions provided in the User Guide to use
colvar. I am using the ubiquitin tutorial as a starting point. In fact,
you might say I am developing a tutorial section for colvar, which I would
be happy to make available (once I figure it out). I am quite frustrated
trying to apply the instructions. the "distance" works fine. But, the next
step for me of RSMD does not work no matter what I do. Here are two things
that I have tried. I have included my working file, which just tracks the
distance between the ends of ubiquitin as an example.
# option 1: put in the atom numbers #
colvar {
rmsd {
atoms { 1 2 3 }
refPositionsFile ubq_ws.pdb
}
}
# option 2: put in the C-alphas #
myatoms {
# add all the C-alphas within residues 1 to 76 of segment "U"
psfSegID U
atomNameResidueRange CA 1-76
}
colvar {
rmsd {
atoms { myatoms }
refPositionsFile ubq_ws.pdb
}
}
Thank you,
Stefan
-- Stefan Franzen Professor of Chemistry North Carolina State University Raleigh, NC 27695 Phone: 919-515-8915 -- Stefan Franzen Professor of Chemistry North Carolina State University Raleigh, NC 27695 Phone: 919-515-8915
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