Re: [AMBER] Partitioning issue of sander

From: David A Case <>
Date: Mon, 16 Apr 2012 09:10:08 -0400

On Mon, Apr 16, 2012, 板垣哲彦 wrote:
> 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 !

Let me add to Jason's answer: this error can arise from a bug in LEaP that
arises when you add crosslinks between polymer chains in a certain way. We
are aware of the problem, but don't have an easy fix.

So, do you have disulfide bonds, or other crosslinks (say between protein and
ligand, etc.) in your system? If not, it's some other problem. If so,
try the parmed ideas Jason mentioned. We might also want to get some details
of your system (probably the input files) to try to find the best fixes and/or


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Received on Mon Apr 16 2012 - 06:30:04 PDT
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