AMBER: Critical patch for pmemd 10 extra points code

From: Robert Duke <>
Date: Thu, 28 Aug 2008 11:20:59 -0400

I have discovered a bug in the pmemd 10 extra points code that will probably
in most instances simply cause a segment violation crash, though you may
want to double check some of your old results. In initialization of extra
points code, a prmtop-related data structure gets rewritten, and under some
conditions, more space is needed than initially specified in the prmtop.
For some compilers/hardware (like my workstations), the bug has no effect;
for others so far I have observed a crash during initialization. I would
recommend applying the attached patch if you use the new extra points
capabilities (eg., tip4p water) for pmemd 10:

Fix: Run this patch from the $AMBERHOME directory, with:
     $ patch -p0 -N -r patch_rejects < pmemd10.patch1

Sorry for any inconvienence; unfortunately testing just didn't expose this
one. No other releases of pmemd are affected, and we will also get the
patch out on the amber website ( soon.

- Bob Duke

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Received on Sun Aug 31 2008 - 06:07:34 PDT
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