On Sun, Feb 03, 2013, Jonathan Saboury wrote:
> So I have this PDB file: http://pastebin.com/VuH7JS5M
>
> and I am run these commands: http://pastebin.com/eVJeJmcP
Oooh, this is a *big* molecule. You will probably have to break it into
fragments.
> What happens is it says "the best APS is not zero, bonds involved by this
> atom are frozen" and gets stuck at "Running: /home/jonathan/amber12//bin/
> sqm -O -i sqm.in -o sqm.out"
SQM is trying to geometry optimize this molecule to a very high
geometrical tolerance, which could take more or less forever. You might
try to drastically relax the geometry tolerance, but examing carefully the
resulting atom types and charges. Better is to split the system into many
smaller fragments (I know: not an easy task).
...dac
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Received on Mon Feb 04 2013 - 09:00:03 PST
