Re: memory allocation in mm_pbsa

From: Holger Gohlke <>
Date: Wed 11 Sep 2002 08:55:07 -0700


> I am using mm_pbsa to post-process a trajectory file made with sander
> (amber7)
> using explicit solvent and PBC (about 41000 total atoms).

Just to make sure - you stripped off water molecules and counter ions
from your snapshots before using mm_pbsa? It's because your value of
ipairs below is close to what I get if I calc 41000 * (41000 - 1) / 2.

> The script
> invokes sander to calculate the
> MM part, but my sistem is too big to get sander working:
> Failed to allocate memory for ipairs: 865675245 (I am using
> This is because the sander input created by mm_pbsa has a cut-off larger
> than
> the system size (99999.0) and there are too many non-bonded pairs.

As Mike noticed some days ago, 99999.0 A might be an overkill. You can
change this number to a value just larger than the largest distance
between atoms in your system (without solvent) in the
"create_sander_input" function in

Best regards


Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
Received on Wed Sep 11 2002 - 08:55:07 PDT
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