AMBER Archive (2008)

Subject: AMBER: PTRAJ - Segmentation Fault

From: dpandit_at_brandeis.edu
Date: Tue Jun 10 2008 - 16:36:08 CDT

Hi All:
I wanted to perform analysis on output trajectory file using ptraj but
I get error of segmentation fault. Below is the error and input file
of ptraj.

Thank you for the help!
Deepa

Error:

[dpandit_at_hpc hGH]$ /share/apps/amber9/exe/ptraj hgh_sol_apr7.prmtop <
merge_mdcrd_reimaged.ptraj > merge_mdcrd_reimaged.out
Residue labels:

   Checking coordinates: eq_pro_hGH.mdcrd
Segmentation fault
[dpandit_at_hpc hGH]$

Input File

trajin eq_pro_hGH.mdcrd
rms first out eq_pro_hGH_rms_bef.out @CA,C,N
center : 1-190
image origin center familiar
trajout eq_pro_hGH_reimage.mdcrd
rms first out eq_pro_hGH_rms.out @CA,C,N
radial rdf 0.5 10.0 :WAT_at_O
strip : WAT
strip : Na+
average avg.pdb pdb
atomicfluct out out bfactor_eq_pro_bfactor.dat byatom bfactor
trajout eq_pro_hGH_reima_strip.mdcrd nobox

Trajectory file
-rw-rw-r-- 1 dpandit dpandit 6442431278 Jun 10 15:30 eq_pro_hGH.mdcrd

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