RE: AMBER: Amber: sander error segmentation fault.

From: Ross Walker <>
Date: Fri, 18 Feb 2005 22:34:22 -0800

Dear Sundar,

> when i ran a sander for minimization it give error as follows.
> segmentation fault,core dumped.i don't know what it mean. but when i

The segmentation fault is due to some kind of division by zero. Note the

      1 6.1081E+08 1.3472E+07 2.4186E+08 O 457

 BOND = 961.4863 ANGLE = 28071.2413 DIHED =
 VDWAALS = ************* EEL = -22338.6619 HBOND =
 1-4 VDW = ************* 1-4 EEL = 5974.0453 CONSTRAINT =

The ****'s mean that the value was too big to fit in the space provided.
Hence you vdwaals and 1-4VDW energies are huge if not infinite. This
indicates that there is something wrong with your initial structure. You
probably have two atoms sitting either very close or on top of each other.
Try using the check function in xleap or alternatively create a pdb from
your prmtop and inpcrd file using ambpdb and then inspect it manually in
something like vmd.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sat Feb 19 2005 - 06:53:01 PST
Custom Search