Hi users
I am having problems with the latest ToolSet version. I tried running "contacts" in ptraj and keep getting a "segmentation fault". I am sending you my input file and log file.
Am I doing something wrong? I also tried using a PDB as input instead of .mdcrd, but it also gave me the segmentation fault.
INPUT:
trajin RNAP_openMD39_42.mdcrd
center :1-2495 mass origin
image origin center familiar
contacts first byresidue out contact.txt time 10 distance 5.0 .CD
go
OUTPUT LOG FILE:
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
MET GLU ILE LYS ARG PHE GLY ARG ILE ARG
GLU VAL ILE PRO LEU PRO PRO LEU THR GLU
ILE GLN VAL GLU SER TYR ARG ARG ALA LEU
GLN ALA ASP VAL PRO PRO GLU LYS ARG GLU
ASN VAL GLY ILE GLN ALA ALA PHE ARG GLU
THR PHE PRO ILE GLU GLU GLU ASP LYS GLY
LYS GLY GLY LEU VAL LEU ASP PHE LEU GLU
TYR ARG LEU GLY GLU PRO PRO PHE PRO GLN
............
............
WAT WAT WAT WAT WAT WAT WAT
PRMTOP does not contain %FLAG RADIUS_SET
Setting box to be an exact truncated octahedron, angle is 109.471221
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin RNAP_openMD39_42.mdcrd
Checking coordinates: RNAP_openMD39_42.mdcrd
./ptraj: line 1: 5109 Segmentation fault ptraj RNAP_open.prmtop
I applied all the new patches, recompiled (gcc on Red Hat enterprise 5) and the ToolSet passed all its test. Even with the patches does ptraj have trouble with large trajectories?? I have since switched over to "netCDF" hoping this will stop the problem.
Steve Seibold, Ph.D.
Assistant Professor of Chemistry
University of Saint Mary
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Received on Mon Feb 21 2011 - 13:00:02 PST
