AMBER Archive (2005)

Subject: RE: AMBER: Error in sander: stack trace terminated abnormally.

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun May 22 2005 - 16:53:36 CDT

> -------------------
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> sander 080D48BE Unknown Unknown Unknown
> Stack trace terminated abnormally.
> ---------------------
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 1000 -4.4953E+07 7.8600E+10 1.8510E+13
> O5' 5143
>
> BOND = 19911.8563 ANGLE = 556.1735 DIHED
> = 1255.4263
> VDWAALS = 45087.7458 EEL = -341302.7317 HBOND
> = 0.0000
> 1-4 VDW = 729.9400 1-4 EEL = ************* RESTRAINT
> = 0.0000
>

You have a bad starting structure, you probably have 2 atoms either on top
of each other or very very close. Note you 1-4 EEL energy is huge, so huge
in fact that it doesn't fit in the space provided in the output file. Your
bond and EEL energies are also huge. I would start by carefully checking
your input file.

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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