On Thu, Mar 27, 2014, Fabian Glaser wrote:
>
> I am trying to use antechamber for a drug, which works great for
> one molecule, but if I use a pdb with two copies of the molecule,
> antechamber never ends:
>
> Total number of electrons: 768; net charge: 0
>
> Running: /Users/fabian/TOOLS/amber/amber12/bin/sqm -O -i sqm.in -o sqm.out
This is a very large system; beyond that, sqm is trying to find an energy
minimum. If you have two molecules, the energy minimum might be with the
molecules arbitarily far apart, and sqm will never complete the job.
Short answer: don't do that. Antechamber is designed to work with single
molecules.
....dac
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Received on Thu Mar 27 2014 - 06:30:03 PDT
