AMBER Archive (2004)

Subject: AMBER: reference with ptraj

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Thu May 06 2004 - 14:50:48 CDT

Hello,

I want to calculate the rmsd against a reference file. Here is the input
file:

trajin annealing.traj 175 200
average average.pdb pdb
rms referernce out allatoms

According to the output file the crd and pdb files are being read but I get
the following message:

ACTIONS
  1> RMS to first frame using no mass weighting
      Dumping RMSd vs. time (with time interval 1.00) to a file named
allatoms
      Atom selection follows [No atoms are selected]

No atoms are selected and I get the rmsd against the first frame. Any idea
what is wrong with the input file?

Many thanks for the help.

John

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