So I have this PDB file: http://pastebin.com/VuH7JS5M
and I am run these commands: http://pastebin.com/eVJeJmcP
For some reason when there is an oxygen atom (carbonyl) it goes haywire (i
tried the same commands with hexane and it simulated fine).
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"
Thanks for the help! :)
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Received on Sun Feb 03 2013 - 21:00:03 PST
