On Fri, May 11, 2012, Asma Abro 28-FBAS/MSBI/F09 wrote:
> We have Amber10 in our lab. So this command won't work for that? Can you
> please help me what else should I follow for Ligand-protein docked complex
> simulation?
You output indicates that you are using AmberTools version 1.x or version 12.
If that is not the case, please go ahead and download AmberTools12 and use
the antechamber that is provided there.
You didn't really say anything about my guess that the problem you are having
arises from having AMBERHOME set to the wrong location. You can certainly use
antechamber to prepare the input files, then use Amber10's sander or pmemd to
run the simulation.
...hope this helps...dac
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Received on Fri May 11 2012 - 11:00:05 PDT
