I am using Amber11/AT1.5. Could anyone point to me how can I get
electrostatic energies in gas phase scaled by dielectric constant with
MMPBSA.py or which variable should I use please? I've read the related part
for MMPBSA.py in the manual, but have not found it.
With the following input, only the polar solvation energy is scaled, while
the electrostatic energies in gas phase stays unaffected.
&general
startframe=1, endframe=1, interval=1,
verbose=2, strip_mdcrd=0, entropy=0, use_sander=1, netcdf=0
/
&pb
indi=2.0, exdi=80.0, scale=2.0, linit=1000, prbrad=1.4,
istrng=0.00, fillratio=4.0, radiopt=0, sander_apbs=0
/
Output:
indi=1.0
EEL -155.0947
EPB 137.9406
indi=2.0
EEL -155.0947
EPB 67.8997
Thanks!
Qiong
On Tue, Jul 24, 2012 at 9:12 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
> Hi All,
> I would like to see the effect of internal dielectric constant in the
> binding free energy calculated by MMPBSA.py. However, putting indi=2, I can
> only get the polar solvation energy scaled 67.8997/137.9406=0.492. But the
> direct electrostatic contribution stays not scaled. I think in order to get
> the direct electrostatic energy scaled, dielectric constant needs to be set
> for sander. However, I have not found the related variable for MMPBSA.py
> input. Although I can manually divide the direct electrostatic energy by
> the internal dielectic constant, it would be better if it could be done
> directly with the script.
>
> Thanks!
> Qiong
>
>
>
>
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Received on Wed Jul 25 2012 - 06:30:02 PDT
