Re: [AMBER] Issue with running sander

From: David A Case <>
Date: Fri, 30 Mar 2012 12:39:47 -0400

On Fri, Mar 30, 2012, 板垣哲彦 wrote:
> vlimit exceeded for step 0; vmax = 29909.5926
> partition error in shake on processor 0
> this processor has atoms 1 through 9100
> atom 9098 is within this range
> atom 9101 is not within this range !

This is a known (but rather rare) bug. Jason should(!) have recognized this,
since he wrote a routine in his new parmed program to fix it.

Basically, LEaP has a restriction that cross links between polypeptide chains
need to contiguous in the sequence; otherwise the atoms per molecule section
of the prmtop file can be wrong. (In other language, a "molecule" that
results from adding a cross link should be continguous in atom numbers.)

The new version of AmberTools12 (due out next week) will have the code that
can fix your problem. But you might also try to rearrange your pdb files
and re-run leap to keep cross-links as close as possible.

[All this assumes that you indeed are adding some cross-links between
polypeptide chains, or between the ligand and protein. If that is not the
case, then something else funny is going on.]


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Received on Fri Mar 30 2012 - 10:00:02 PDT
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