Re: AMBER: bug in reprocessing with PB?

From: Carlos Simmerling <>
Date: Thu, 10 May 2007 14:14:08 -0400

just to add my experience: we have had the same problem
for a long time, postprocessing using PB is very unreliable.

On 5/10/07, David Mobley <> wrote:
> All,
> I'm doing some studies to compare implicit solvent models in AMBER,
> and I believe I've found a bug of some sort.
> In particular, I have a set of trajectory files and I need to evaluate
> energies of the snapshots from these trajectories in different
> implicit solvent models. Mostly, this works fine (using sander with
> imin=5 to evaluate energies of a stored trajectory). However,
> sporadically, when I use PB for reprocessing, I get segmentation
> faults during reprocessing for no apparent reason. The trajectories
> seems to be OK (i.e., reprocessing with GB works fine).
> Sometimes, these segmentation faults are architecture-dependent (i.e.
> I'm mainly on Xeons; stuff that fails there will work OK, sometimes,
> on Opterons). However, I'm attaching a tarball for one case that fails
> (with PB) on either architecture. Again, it reprocesses fine using GB.
> I'm really at a loss here -- I desperately need this reprocessing to
> work -- so I will greatly appreciate any help. Just grab the tarball
> and run the "" shell script, which executes sander to do the
> reprocessing that's causing the seg fault.
> Thanks,
> David
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun May 13 2007 - 06:07:28 PDT
Custom Search