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.
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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
mask
:1-102,104-129,136-139,141-146,154-191,192-195,197-211,221-232,234-303,308-399_at_CA
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
