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
<eof>
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
