AMBER Archive (2007)

Subject: AMBER: ptray segfault: vector out

From: Nicolas Lux Fawzi (fawzin_at_berkeley.edu)
Date: Thu Jun 21 2007 - 14:19:49 CDT

Hi amber folks

I'm trying to use the vector function of ptraj. I was interested in
the output of the vector command before any analysis
The following ptray script give me a segfault. Please let me know if I
am doing something wrong.

ptraj script:
_____________
$ cat ptrajscript_vector
trajin mdcrd

strip :WAT

vector v0 @5 corr @6 order 2 out rawvectorv0.out
#analyze timecorr vec1 v0 tstep 1.0 tcorr 100.0 drct dplr out v0.out
________________

one thing is that if I get rid of the "out rawvector0.out" of the
vector command, it works fine
the following line starting with analyze also seems to work fine, even
when the above vector out is specified.

I am running amber9 with all the bugfixes compiled with pathscale suite
on centos 4 linux running on amd opterons

the fault looks like below:
_______________________________________________

PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin mdcrd
   Checking coordinates: mdcrd

PTRAJ: strip :WAT
Mask [:WAT] represents 6316 atoms

PTRAJ: vector v0 @5 corr @6 order 2 out rawvectorv0.out
Mask [@5] represents 1 atoms
Mask [@6] represents 1 atoms
[No output trajectory specified (trajout)]

PTRAJ: Successfully read the input file.
        Coordinate processing will occur on 2000 frames.
        Summary of I/O and actions follows:

INPUT COORDINATE FILES
   File (mdcrd) is an AMBER trajectory (with box info) with 2000 sets

NO OUTPUT COORDINATE FILE WAS SPECIFIED

ACTIONS
   1> STRIP: 6316 atoms will be removed from trajectory: :12-1590
   7> VECTOR: storage to array named v0
       Calculate the vector between the center of mass of the two atom
selections
       which follow (with the origin at the center of mass of the first)
       Atom selection 1 is :1_at_CA
       Atom selection 2 is :1_at_HA
       The order of Legendre polynomials is 2
       Output will be dumped to a file, rawvectorv0.out

Processing AMBER trajectory file mdcrd

Set 1 .................................................
......
Set 1900 .................................................
Set 1950 .................................................
Set 2000

PTRAJ: Successfully read in 2000 sets and processed 2000 sets.
        Dumping accumulated results (if any)

PTRAJ VECTOR: dumping vector information v0
Segmentation fault

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