AMBER: ptraj

From: Wen Li <>
Date: Thu, 8 Jul 2004 12:06:01 -0400 (EDT)

Hello All,

I am trying to do trajectory analysis using ptraj (matrix). My trajectory
file was generated from AMBER7/sander (PME), and it recorded the
coordinates of one macromolecule and Na+/Cl- ions (not recorded that of
water molecules). I wonder if I should use a topology file consisting of
the molecule and the ions or the molecule only - actually resulted in
the same error message: Segmentation fault (core dumped).

The following are what I did and used. I was hoping that you could help

/usr/local/fbscapp/amber8/exe/ptraj <
or /usr/local/fbscapp/amber8/exe/ptraj <

trajin mytrajectory
#strip:Cl- (tests stripping ions and not did not work)
rms first *
matrix covar name mcovar out mcovar.dat
analyze matrix mcovar out evec.pev vecs 25

Wen Li

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Received on Thu Jul 08 2004 - 17:53:00 PDT
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