Hi
I am bachelor and tried to calculate rmsd about trajectory of remd.
In order to calculate rmsd, I looked at amber tutorial about rmsd.
but what I want to calculate is not in your tutorial rmsd.
I hope that not first structure but native structure that I downloaded in
www.pdb.org ( not calculate the minimization).
Could you tell me that what to do?
Sincerely,
Choonki Kim
The precise parameter we will be calculating in this example is the mass
weighted RMSd fit between each successive structure and the *first
structure of our trajectory.* This is done by providing an input file to
ptraj containing a list of commands describing the relevant files and what
we want it to do etc.:
trajin polyAT_vac_md1_12Acut.mdcrd
rms *first* mass out polyAT_vac_md1_12Acut.rms time 0.1
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Received on Fri Sep 06 2013 - 20:00:02 PDT
