Re: AMBER: nmode with ibelly

From: David A. Case <>
Date: Mon, 6 Jun 2005 13:09:08 -0700

On Mon, Jun 06, 2005, Martin Sippel wrote:
> using nmode in amber8, I want to do some entropy calculations on a
> protein-ligand-complex. The system is pretty large, hence I employ the
> ibelly-option to fix the major part of my protein, but even with only two
> residues allowed to move, nmode still gives the "segmentation fault" error
> message, nothing else. I have 2 gigs of memory, so that should be no
> problem.

Amber's nmode does not currently reduce the space requirements based on the
belly specification; see lines 90-100 of $AMBERHOME/src/nmode/nmode.f.

I am not quite sure why you are getting segmentation faults. The allocation
statements (lines 104 and 107 of the above file) should exit cleanly with
a useful error message if enough space is not available. We need to figure
out why this doesn't happen.


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Received on Mon Jun 06 2005 - 21:53:00 PDT
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