AMBER Archive (2004)

Subject: AMBER: Using pbsa

From: Thomas Steinbrecher (
Date: Tue Apr 20 2004 - 18:16:37 CDT

Dear Amber users,

I am trying to do MM-PBSA calculations on a protein (~25kDa) ligand
complex, using amber8 on Redhat Linux. I use as provided in
the examples, except that I had to set radioopt to 0 because my ligand
contains gaff-atomtypes.

When I let run over my snapshots, the pbsa calculation fails
always at the same complex snapshot.

The last line in the pbsa*.out contains this error message:

PB Bomb in epsbnd(): No neighbor found for exposed boundary grid 22
          60 16

The snapshot where the calculations fails is not visibly different from
the one before (rms <1.5A)

Can anyone tell me what this error means or how to fix it?

Kind regards,


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