AMBER Archive (2004)

Subject: Re: AMBER: RSM & ptraj

From: Elijah Gregory (ejgregory_at_gmail.com)
Date: Sun Oct 31 2004 - 01:29:23 CDT

   You need to load in each trajectory with four trajin commands in
one input file and then issue an rms command. This should calculate
the rmsd from the first structure of the first run for all four
trajectories in succession.
   
   What you are doing is taking the first run and calculating the rmsd
from the first structure in that run, then loading in the second run
and calculating the rmsd from the first structure of *that* run, etc.
Obviously the "distance" between the first structure in a run and the
first structure in a run will be zero.

Try using this input file:

model1-3mdCA-rms.in

trajin model1-3-md1.crd
trajin model1-3-md2.crd
trajin model1-3-md2a.crd
trajin model1-3-md2b.crd
rms first out model1-3md-backbone.rms @CA time 0.2
strip :WAT
go

Hope this helps,

   Elijah Gregory
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