AMBER Archive (2004)

Subject: AMBER: ptraj

From: Wen Li (liw_at_wadsworth.org)
Date: Thu Jul 08 2004 - 11:06:01 CDT

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
me.

/usr/local/fbscapp/amber8/exe/ptraj nowater.top < ptraj.in
or /usr/local/fbscapp/amber8/exe/ptraj nowater_noions.top < ptraj.in

ptraj.in

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

Thanks,
Wen Li

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