> 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.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu May 06 2004 - 21:53:00 PDT
