AMBER: rms and rms nofit

From: Alana Canfield <>
Date: Sat, 8 Sep 2007 17:23:39 -0400 (EDT)

Dear Amber Users,

I would like to perform a rmsd calculation in ptraj for my protein
complex, and then I would like to use the fit from that first rms
calculation to perform a rmsd calculation on just the interface. My mask
must change, but I want to keep the old fit from the previous rms command.
 The regular fit alone works fine, but if I add a second rms fit I get a
segmentation fault. Any advice to help me see how else to arrange this
would be appreciated.
My input file:

  trajin /home/acanfield/hGH/prod1/md_prod1.traj
  trajin /home/acanfield/hGH/prod2/md_prod2.traj
  trajin /home/acanfield/hGH/prod3/md_prod3.traj

  reference /home/acanfield/hGH/heat1/hgh_min4.rst

  trajout /home/acanfield/hGH/process/interface_nofit/prod.traj nobox

  strip :WAT


  strip :103,130-135,140,147-153,196,212-220,233,304-307

  rms reference .CA time .15 name rmsd

  mask :1-19,54-74,167-191_at_CA

  rms reference out /home/acanfield/hGH/process/interface_nofit/rmsd.out
:1-19,54-74,167-191.CA time .15 name rmsd nofit

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Received on Sun Sep 09 2007 - 06:07:48 PDT
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