AMBER Archive (2008)

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

From: Jose Borreguero (borreguero_at_gmail.com)
Date: Fri Sep 05 2008 - 10:06:42 CDT

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:
   *NSTEP ENERGY RMS GMAX NAME NUMBER
  20150 -5.7069E+04 1.1228E-03 4.5015E-02 H1 9884

 BOND = 4411.3524 ANGLE = 93.5743 DIHED =
212.3167
 VDWAALS = 10160.1516 EEL = -75579.7172 HBOND =
0.0000
 1-4 VDW = 156.0090 1-4 EEL = 3475.8361 RESTRAINT =
1.9324
 EAMBER = -57070.4772*
And here's the input file:
 *&cntrl
     imin=1, maxcyc=100000, ntmin=0, ntr=1,
     cut=10.0, nsnb=10, ntc=1, ntf=1, drms=0.0005
 &end
#Apply restraints to the solute atoms
 1.0
RES 55 63
END
END*
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
Email: borreguerojm_at_ornl.gov

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