Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy

From: Jason Swails <>
Date: Wed, 06 Nov 2013 08:41:31 -0500

On Wed, 2013-11-06 at 21:18 +0800, David Chen wrote:
> I got error message on terminal:
> mmpbsa_py_energy: malloc.c:2451: sYSMALLOc: Assertion `(old_top ==
> (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) - __builtin_offsetof
> (struct malloc_chunk, fd)))) && old_size == 0) || ((unsigned long)
> (old_size) >= (unsigned long)((((__builtin_offsetof (struct malloc_chunk,
> fd_nextsize))+((2 * (sizeof(size_t))) - 1)) & ~((2 * (sizeof(size_t))) -
> 1))) && ((old_top)->size & 0x1) && ((unsigned long)old_end & pagemask) ==
> 0)' failed.

Well that's a strange error message. I'm not sure why malloc would
raise an error like this in a GB calculation. GB is not very
memory-intensive, so it's highly unlikely that your machine is running
out of RAM unless you are using a queueing system (torque/PBS, slurm,
etc.) which has a low memory limit on the job. If this is the case, you
can try to request more memory and see if that helps.

Perhaps your installation got corrupted somehow. Can you try
re-compiling AmberTools and running again? (Make sure to apply all
updates, although no updates were specifically targeted for a problem
with mmpbsa_py_energy)

You can also add use_sander=1 to the &general section of the
input file to try using sander instead (assuming you have Amber 12
installed, too).

The last thing I can think of is that maybe your topology files are
either bad or in some other way unsupported by NAB (but unless your file
is something like an amoeba topology file or some other non-standard
form, this scenario is unlikely).

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Nov 06 2013 - 06:00:03 PST
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