Re: [AMBER] Partitioning issue of sander

From: David A Case <>
Date: Tue, 17 Apr 2012 09:20:05 -0400

On Tue, Apr 17, 2012, 板垣哲彦 wrote:
> > setBond :83.NE2 :575.FE 60 2.01
> MoleculeError: Molecule atoms are not contiguous!

You need to rearrange your input pdb file so that the iron and oxygen that
will be bonded to the first subunit come immediately after the first subunit;
same for subsequent subunits. Don't put the irons or the oxygens all at the
end. Basically, atoms that are going to become part of a single molecule need
to be continguous in atom number.

...good luck...dac

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Received on Tue Apr 17 2012 - 06:30:06 PDT
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