On Fri, Aug 07, 2009, Scott Pendley wrote:
>
> I am attempting to calculate the free energy of solvation for several small
> organic molecules. I want to use nmode to calculate entropic contributions
> in the gas phase (or vaccuum phase) and was having trouble finding a listing
> of the variables that can be passed to the nmode program. I have modified
> the input script from the MM-PBSA program slightly as follows
>
> File generated by mm_pbsa.pl
> &data
> ntx = 0,
> ntrun = 1, nvect = 0,
> drms = 1000,
> dielc = 1.0, idiel = 1,
> scnb = 2.0, scee = 1.2,
> t = 298.0
> &end
> END
>
> The presence of external and internal dielectic variables suggests that
> nmode would be operating under the assumption of continuum solvent which
> would not be present in vacuum phase simulations. Any suggestions on
> modifications to the input script or approaches to make this calculation?
The above looks fine. The combination dielc=1 and idiel=1 implies a vacuum
simulation. Be sure to check that you get the same energies in nmode as in
sander.
We are in the process of retiring nmode, in favor of NAB, which offers more
flexible and powerful normal mode options. But the MM-PBSA script has not yet
been updated. If you go the Amber web site and look for the Amber 9 Users'
Manual, you can get a description of the input variables.
...dac
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Received on Wed Aug 19 2009 - 21:04:45 PDT
