Hi,
A while ago the following error was reported for pb calculations
performed by a nab program:
pb_fdfrc(): Atom out of focusing box
see the post here
http://archive.ambermd.org/201103/0189.html
The symptoms include that if the "problem" frame is used in isolation,
the error does not occur, but when part of a trajectory the error
occurs.
I'm having the same problem, except in sander. When I use the
mmpbsa_py_energy program, I have no problem. When I use
sander I get the focusing error. I notice that mmpbsa_py_energy
produces Reaction Field Energy values every step, while sander does
not. Maybe the grid is not being recalculated?
The files to reproduce the problem are here:
http://www.amber.utah.edu/biodata/sander-pbsa-problem/
sander produces the error with frames_1-3.traj but not frames_2-3.traj.
mmpbsa_py_energy works with both. (Fully patched Amber 11, AT 1.5)
Thanks for any help,
--Niel
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Received on Thu Oct 13 2011 - 20:30:02 PDT
