AMBER Archive (2004)

Subject: Re: AMBER: reference with ptraj

From: Thomas E. Cheatham, III (
Date: Thu May 06 2004 - 15:11:58 CDT

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

No reference structure was specified (and reference is spelled wrong).

Currently ptraj only goes through the trajectory once, so to get the RMSd
to the average structure is has to be done in two runs, the first to
generate the average structure

  trajin annealing.traj 175 200
  average average.pdb pdb

and then

  trajin annealing.traj 175 200
  reference average.pdb
  rms reference out allatoms *

> 1> RMS to first frame using no mass weighting

reference was spelled wrong, but it wouldn't have worked anyways since the
reference structure was not referenced...

> Atom selection follows [No atoms are selected]

Hmmn, it should have been all atoms. You can try adding a "*" after the
rms command as shown above.

Good luck.
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