On Wed, May 02, 2012, Marek Maly wrote:
> I repeated calculation of dG_bulk_elec of phenol using input files from
> tut. A9 and have obtained value -38.49138 kcal/mol which is almost
> identical with the previously reported value ( -38.64 see below) which
> is really different from the value reported in below mentioned article (
> -6.03 kcal/mol).
If dG_bulk_elec refers to phenol in bulk water, then this number is way wrong
(as you point out). It was kind of hard to follow the scripts to supplied,
but I don't see where you are computing the electrostatic change in vacuum:
this needs to be subtracted from the charging free energy in water to get the
electrostatic contribution to the solvation free energy.
[The "softcore" code makes this vaccum step unnecessary, but you don't seem
to be using that option(?)]
...hope this helps....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 05 2012 - 07:00:03 PDT
