AMBER Archive (2008)

Subject: RE: AMBER: help...sander "segmentation fault" after 2hours of minimization

From: Ross Walker (
Date: Fri Sep 05 2008 - 10:23:42 CDT

Hi Jose,


There doesn't look to be anything wrong here, although a bond energy of 4411
is pretty high, but then it is not clear how many atoms you have etc. I
suspect the minimizer has gone as far as it can and should quit with a
linmin error (your RMS is pretty low). However, it should not segfault.


Is this in serial or parallel? Which version of AMBER are you using and have
you applied all the bug fixes? Do all the test cases pass?


All the best



From: [] On Behalf Of
Jose Borreguero
Sent: Friday, September 05, 2008 8:07 AM
To: amber mailing list
Subject: AMBER: help...sander "segmentation fault" after 2hours of


Dear Amber users,
I am trying to understand what went wrong with my minimization. The last
lines of the output file do not indicate anything weird going on, or maybe
the BOND energy term is indicating somethin (at the beginning of the
minimization, BOND=115.7477 and at the end, BOND=4411.3524 ).
Where else should I look for pointers to the problem?
Here are the last lines of the output file:
  20150 -5.7069E+04 1.1228E-03 4.5015E-02 H1 9884

 BOND = 4411.3524 ANGLE = 93.5743 DIHED =
 VDWAALS = 10160.1516 EEL = -75579.7172 HBOND =
 1-4 VDW = 156.0090 1-4 EEL = 3475.8361 RESTRAINT =
 EAMBER = -57070.4772
And here's the input file:
     imin=1, maxcyc=100000, ntmin=0, ntr=1,
     cut=10.0, nsnb=10, ntc=1, ntf=1, drms=0.0005
#Apply restraints to the solute atoms
RES 55 63
Best regards,

Dr. Jose M. Borreguero
Postdoctoral Associate
Oak Ridge National Laboratory
P.O. Box 2008, M.S. 6164
Oak Ridge, TN 37831
phone: 865-241-3071 fax: 865-576-5491

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