[AMBER] Fwd: amber

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Fri, 31 Jan 2014 21:25:38 -0800

Hi all,

I am trying to compute the rmsd to an average pdb - I am using the follow
input for ptraj as described below - the problem is that the reference does
not seem to exist for the rmsd calculation:

# We use this template
trajin mdcrd1
trajin mdcrd2

# Remove water
strip :WAT

center origin :1-222
image origin center

# get an average pdbfile from the "new" reference
# frame to use to with grid.lis from the last step
# to display
average avg.pdb pdb
# want to set the reference as the average pdb
reference avg.pdb

# need rms to remove rotation and translation
rms first mass :1-222
rms reference out PHE_135_rmsd.dat :135

Any suggestions how to fix this - thanks.
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Received on Fri Jan 31 2014 - 21:30:02 PST
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