[gmx-users] Bug in g_chi -p?

Justin A. Lemkul jalemkul at vt.edu
Sat Sep 26 18:06:33 CEST 2009


I'm trying to calculate order parameters from g_chi for a protein complex with 
bound ligand.  I'm using version 4.0.5, and if I specify the -p option, the 
program gives a Bus error without writing all the output:

g_chi -s ./0_10ns/md_0_10.tpr -f fix_400.xtc -o -jc -g -p


130 residues with dihedrals found
560 dihedrals found
Last frame      40000 time 400000.000
j after resetting (nr. active dihedrals) = 390
WARNING: not all dihedrals found in topology (only 390 out of 560)!
Now calculating transitions...
Total number of transitions:     156047
Time between transitions:       999.724 ps
Bus error

 From the above, I get Jcoupling.xvg and order.xvg, but chi.log is empty and I 
do not get the requested order.pdb.  If I omit -p, chi.log is written.

Is there a known issue using the -p flag in g_chi?  Is this potentially a bug, 
or am I using the command wrong?

I should also mention that the issue occurs on both our cluster (PowerPC 
architecture, Mac OS X 10.3.9) as well as my personal machine (Intel MacBook 
running OS X 10.5.8).

Thanks for your attention.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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