AMBER Archive (2004)

Subject: AMBER: question about Ptraj - AND OR

From: james tomomi macdonald (
Date: Mon Jul 12 2004 - 10:06:59 CDT


Using the mask in ptraj (from the Amber 8 distribution), how do you, for
example, select @CA,C,N AND :10-80

I tried

rms reference out rms_test @CA,C,N,:10-80

however that selects:

  1> RMS to reference structure (./pdbs/bb2n_500K.pdb.2874) using no
mass weighting
      Dumping RMSd vs. time (with time interval 1.00) to a file named
      Atom selection follows :1-9_at_N,CA,C,:10-80,:81-89,N,CA,C

which is not what i want. I would like the N, CA, and C atoms of
residues 10-80 and nothing else.

I apologise if this is in the manual, but i couldn't find it.



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