On Wed, Apr 13, 2016 at 12:37 PM, Cortopassi, Wilian <
wilian.cortopassi.chem.ox.ac.uk> wrote:
> Dear Amber12 users,
>
> I am trying to set up a MMGBSA calculation with a dielectric constant of 4
> but Amber12 is not recognising the "intdiel" variable.
>
> I have seen some people discussing the same problem in:
>
> "Re: [AMBER] mmPBSA.py: mmGBSA and solute dielectric constant"
>
> I tried to use -make-mdins and then to add intdiel=4 in the _MMPBSA_gb.mdin
> file, but I still get the same error:
>
> "Unknown variable intdiel="
>
​First, it's important to understand *why* intdiel is not an input option
for GB calculations. That is, the "1" in the GB equation is the dielectric
constant of the medium you are transferring from, not the dielectric
constant of the interior of the solute (unlike PB, where the interior
dielectric *is* the dielectric of the solute). So changing this to 2 or 4
means that what you are actually calculating is the solvation free energy
of transferring your molecule from a low-dielectric solvent (like
cyclohexane, for instance) into water.
If you really want to modify the internal dielectric constant, I suggest
using PB instead of GB.
That said, the problem here is that, by default, MMPBSA.py uses a nab
program to compute GBSA energies, and nab does not support intdiel at all.
You also need to add use_sander=1 to the &general section of your MMPBSA.py
input file.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Apr 13 2016 - 10:00:05 PDT
