AMBER: Amber 8 ptraj segmentation fault

From: Sivakolundu, Sivashankar <>
Date: Wed, 7 Apr 2004 00:49:08 -0500

Hi amber users,

I'm trying to do a normal mode analysis of an Amber trajectory (generated using Amber 7) using the utilities in the ptraj of Amber 8. I followed the example in the manual with few modifications to do the calculation. My instruction file for ptraj is given below

trajin in.mdcrd #in.mdcrd has been superimposed using ptraj
trajout out.mdcrd
matrix covar name covmat .CA out covariance.dat
analyze matrix covmat name evecs out evecs.dat vecs 200
projection modes evecs.dat out project.dat beg 1 end 1 .CA start 1 stop 600

ptraj executes every of the above commands completely except for the last command (projection). when it executes projection modes command, it gives a segmentation fault and crashes. The output file of the projection mode... command contains,

Projection of snapshots onto modes
  Snapshot Mode1
         1 -130.282
         2 45.428
         3 -80.964
         4 -117.678
       599 53.619
       600 93.868

I'm worried about the source of the segmentation fault. The topology file and the trajectory file has the same # of atoms. Can anyone think of what I might be doing wrong? My other question is where does ptraj dump the projection coordinates? Does it dump in file specified in trajout command?

Thank you very much for your input

Siva Sivakolundu

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Received on Wed Apr 07 2004 - 07:53:00 PDT
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