On Mon, Feb 23, 2015, Martin Olsson wrote:
>
> I am trying to set up free-energy perturbation calculations using the
> ff02 force field...
> using the RESP method. http://www.teokem.lu.se/~ulf/Methods/resp.html
>
>
> I have access to a compiled version of Amber 14 on the cluster I am
> using, why it would be preferable to use that if possible, but I do not
> know the details of how to amend the sander.in namelist input.
Generally, you need to set ipol=1; other parameters are mostly the same as for
a non-polarisable force field. The 2002 force field is rarely used (as far as
I can tell), and is described under "obsolete force fields" in section 3.12.4
of the Amber14 Reference Manual. Also look at section 17.7.5 (on "polarizable
potentials"). Some examples are in amber14/test/dna_pol and
amber14/test/polarizable_water.
>
>
> Is there a dependency on AMOEBA for Amber 14? I am receiving the error
> message AMOEBA_get_ucell_info: UNIT_CELL_PARAMETERS missing
>
> in my sander.out file . The error was previously posted in Amber mailing
> list archive: http://archive.ambermd.org/200806/0296.html
Do you have iamoeba set in your input file? If so, remove it: you don't
want that for ff02; if not, we will need more details.
....dac
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Received on Mon Feb 23 2015 - 09:00:03 PST
