Re: AMBER: Critical patch for pmemd 10 extra points code

From: Carlos Simmerling <>
Date: Sun, 31 Aug 2008 09:54:33 -0400

Bob- just to clarify, is the only potential problem a crash? in other
words, if we have run a lot of sims with this code and gotten no
crash, is it ok or are the potential problems with the data?

On Thu, Aug 28, 2008 at 11:20 AM, Robert Duke <> wrote:
> 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

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:
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Received on Wed Sep 03 2008 - 06:07:08 PDT
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