AMBER Archive (2007)

Subject: AMBER: vector corrplane

From: Servaas Michielssens (servaas.michielssens_at_student.kuleuven.be)
Date: Thu Aug 02 2007 - 10:25:45 CDT

I used following script in ptraj:

trajin /temp0/servaas/valrep/amber1mdcrd.000
vector v0 :CYG_at_C11,C12,C13 corrplane out test

This is the output:

PTRAJ: vector v0 :CYG_at_C11,C12,C13 corrplane out test
Mask [:CYG_at_C11,C12,C13] represents 3 atoms
FYI: No output trajectory specified (trajout), none will be saved.

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 600 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (/temp0/servaas/valrep/amber1mdcrd.000) is an AMBER trajectory (with box info) with 600 sets

OUTPUT COORDINATE FILE
  NULL entry

ACTIONS
  1> VECTOR: storage to array named v0
      Calculate the vector perpendicular to the least squares best plane
      through the atom selection which follows
      Atom selection is :61_at_C11,:61_at_C12,:61_at_C13
      The order of Legendre polynomials is 2
      Output will be dumped to a file, test

Processing AMBER trajectory file /temp0/servaas/valrep/amber1mdcrd.000

Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250 .................................................
Set 300 .................................................
Set 350 .................................................
Set 400 .................................................
Set 450 .................................................
Set 500 .................................................
Set 550 .................................................
Set 600

PTRAJ: Successfully read in 600 sets and processed 600 sets.
       Dumping accumulated results (if any)

PTRAJ VECTOR: dumping vector information v0
Segmentation fault

And at the end their is a crash. I don't see wat the problem is.

thanks for your help,

kind regards,

servaas

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