[AMBER] QM/MM cut problem

From: <aapeters.ncsu.edu>
Date: Tue, 20 Apr 2010 12:36:18 -0400 (EDT)

Hello users

When using Amber10 QM/MM I get errors complaining my box is too small.

But when I look at the structure and at the QM region coordinates, there
seems to be enough space. There seems to be a conflict between the
coordinate extremes written out in the first part of the output file (or
the qmmm_region.pdb file), and the bounds written out in the latter part
of the output file:

  ERROR: QM region + cutoff larger than box dimension:
  QM-MM Cutoff = 4.0000
   Coord Lower Upper Size Radius of largest sphere inside unit
     X -5.632 13.150 18.782 11.146
     Y -5.431 13.671 19.102 11.146
     Z -15.168 14.794 29.962 11.146

To hone in on the problem, I set up a run that crashes on the second step.
1) the initial qm region positions are written in the output file
2) the system takes one step, and writes "qmmm_region.pdb", the
corresponding pdb file
3) the system crashes on the 2nd step, writing the bounds violation in the
output file.

Assuming positions barely change in one step, there seems to be a
significant conflict within the code about where it thinks the bounds are?

I attached the output files

Thanks in advance for any help.

Andrew Petersen

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Received on Tue Apr 20 2010 - 10:00:03 PDT
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