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AMBER Archive (2004)Subject: Re: AMBER: reference with ptraj
From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
> trajin annealing.traj 175 200
No reference structure was specified (and reference is spelled wrong).
Currently ptraj only goes through the trajectory once, so to get the RMSd
trajin annealing.traj 175 200
and then
trajin annealing.traj 175 200
> 1> RMS to first frame using no mass weighting
reference was spelled wrong, but it wouldn't have worked anyways since the
> Atom selection follows [No atoms are selected]
Hmmn, it should have been all atoms. You can try adding a "*" after the
Good luck.
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