Re: seg fault

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Sep 16 2003 - 16:22:44 CDT

Hi Cheri,

Jim is right, after looking at your logfile and seeing the energies, no
wonder namd is choking...

Warning: Not all atoms have unique coordinates.
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT
VDW BOUNDARY MISC KINETIC
       TOTAL TEMP PRESSURE GPRESSURE VOLUME PRESSAVG
GPRESSAVG
ENERGY: 0 13373540.4319 99999999.9999 1986.8588 99999999.9999
-111162.1731 5796362.1421 0.0000 0.0000 0
.0000 99999999.9999 0.0000 99999999.9999 99999999.9999
429831.6119 99999999.9999 99999999.9999
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
SEGMENTATION FAULT

The sun doesn't get this hot!

There are to atoms bonded together in the psf file that are on top of each
other in coordinate space.

Looking at your pdbfile I see that all the heme hydrogen atoms have no
coordinates, they are all sitting at 0 0 0

I thought Heme wasn't in here?

Brian

-- 
*****************************************************************
**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1_at_llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
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