Dear Amber users,
I've been running some MMPBSA calculations and I encounter the following
problem: my system seems to be exploding.
I extracted snapshots from my trajectory of 1000ps and run the mmpbsa
receptor-ligand binding free energy calculation. The system behaves
normally until and including snapshot 127. After that everything
explodes and I get the error:
> SA Bomb in sa_arc(): Allocation aborted
I've tried using fill ratio 2.0, 3.0 but not change. I tried using
different number of snapshots 150, 200, 250. Same problem.
I've looked at the trajectory and it looks perfectly normal for the
entire run of 1000 ps.
If I use only 100 snapshots for the 1000ps trajectory, the systems
behaves perfectly.
I've split my trajectory in batches of 250 ps and extracted snapshots
from them. Everything runs normal. However if I want to use all of them
in one go. My systems is getting messy at the 128th snapshot.
I've read the archive posts relating to the SA Bomb, but I could not
come to any conclusion as to what is happening in my system.
Any ideas would be highly appreciated.
Cristina
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Received on Wed Jun 16 2010 - 08:00:04 PDT
