AMBER Archive (2004)

Subject: AMBER: question about the average structure from ptraj

From: aini_at_UMDNJ.EDU
Date: Sun Feb 08 2004 - 13:33:23 CST

Dear Ambers,

  I used ptraj to generate average structure for my simulation. I noticed
the orientation sidechain of one residue was distorted a lot compared with
initial input structure. However, when I viewed my trajectory file using
VMD, the sidechain of that residue was in the same orientation as in the
input file. Anyone has many clues here about what might be the problem?

ptrajin file is here
ptraj << EOF
average AR.agonist.average.pdb start 1 stop 200 offset 1 pdb nowrap nobox


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