Dear Amber users,
I am trying to do MM-PBSA calculations on a protein (~25kDa) ligand
complex, using amber8 on Redhat Linux. I use mm_pbsa.in as provided in
the examples, except that I had to set radioopt to 0 because my ligand
contains gaff-atomtypes.
When I let mm_pbsa.pl 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,
Thomas
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Received on Wed Apr 21 2004 - 00:53:01 PDT
