AMBER: problems with bonds in sander

From: Fabien CAILLIEZ <>
Date: Thu, 7 Jul 2005 20:18:19 +0200 (CEST)

Dear AMBER users,

I have a problem with sander with one particular topology file. This is a
topology file that I created by modifying an output file from Leap. The
only things I did is add some new bonds without hydrogen and modify
Lennard-Jones parameters.

When I use the topology file created by Leap, everything is fine. But with
the modified file, I get this error message :
MPI: On host, Program
/gt/lib1/Library/amber8/exe/sander, Rank 0, Process 64885455 received
signal SIGBUS(10)

MPI: --------stack traceback-------
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 10

I found the origin of the problem but cannot understand why it is a
problem. It comes from one particular bond that I created between atoms 2
and 50 (indices 3 and 147 in the %FLAG BONDS_WITHOUT_HYDROGEN part of the
topology file).
Here is the line defining the bond in the topology file :
       3 144 21 3 147 22 6 9 23

When I replace atom 50 by another atom in this bond (the atom 50 is the
last atom of my structure), it works fine. It also works fine if I replace
this atom 50 in some other bonds (but not all). I really do not understand
this behavior.

I would appreciate any help.
Thanks in advance,
The AMBER Mail Reflector
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Received on Thu Jul 07 2005 - 19:53:00 PDT
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