On Mon, May 09, 2011, r smith wrote:
>
> I was wondering whether, when using the amoebapro.prm parameter file, does
> sander read the specifications in the header of the .prm file which describe
> the potential energy functional forms (e.g.,forcefield, vdwtype, etc.),
> scaling (e.g., vdw-14-scale), etc. Is it true that the default amoeba
> specifications would be used by sander despite the header of the
> amoebapro.prm file, and only the parameter info in the .prmtop is read?
I don't know the answer, but can't you run some experiments yourself? Make
changes in the amoebapro.prm file, and see what happens to the prmtop?
(Sander only reads the prmtop file, nothing else, if that is what you are
asking.)
....dac
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Received on Thu May 12 2011 - 08:30:02 PDT
