On Tue, Apr 07, 2009, Tomasio, Susana wrote:
>
>
> Sorry, but basically what I am not understanding is the relation between
> Run.amoeba and Run.amoeba_sol and the files that I need to run the
> simulation. Can I just start with the file jac_2.pdb and create the
> box, solvate, save the amoeba parameters and then run a simulation with
> sander?
Yes, what you describe is supposed to work, and the reason for your
failure needs to be tracked down.
As Wei suggested, try running Run.amoeba_sol, and using the hpv files it
creates in a sander run. Knowing whether or not that works should help
narrow down the source of your problems.
...thx...dac
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Received on Wed Apr 08 2009 - 01:19:56 PDT
