I am sorry Dr. Case, I am not getting this thing that how the AMBERHOME is
set to wrong location? Actually I am just going to run my first simulation
so I really don't have the detail idea of these things.
I'll install ambertools12 as we have an older version. Thanks for your
suggestions.
On Fri, May 11, 2012 at 10:45 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 - 23:30:03 PDT
