Re: [AMBER] mmGBSA and solute dielectric constant

From: Changqing Yan <>
Date: Thu, 4 Jul 2013 23:19:11 +0800

Hi Jason,
I think I can get your meaning but I cannot put it into practice. Since
when I run again, a new _MMPBSA_gb.mdin file was generated and inside there
are no longer the term which I add. would you lease specify how I can
achieve what you mean?
My input file was:
Input file for running PB and GB&general endframe=2000,interval=40,
 keep_files=0, receptor_mask=:1-682:688-694,
 ligand_mask=:683-687,verbose=2, strip_mask=:WAT:Na+, use_sander=1,/&gb

and my script to run is
pbs_mpirun $AMBERHOME/bin/ -O -i -o
mmpbsaigb5e4md2-3.dat -sp ...

My procedure is to run the script, and then Cntrl+C when the
_MMPBSA_gb.mdin was formed. And I changed the
_MMPBSA_gb.mdin file and then run the script again.


From: Jason Swails
Date: Wed, 30 Jan 2013 22:00:06 -0500

By default uses a NAB program to calculate the GB potential. NAB
actually does not allow the internal dielectric constant to be changed (see
the epsext variable description on page 421 of the manual).

If you are so inclined, you can force to use sander (set
use_sander=1 in the &general section of the input file), then use
-make-mdins to generate the GB mdin file, add intdiel=2 or 4 to the &cntrl
namelist there (typically _MMPBSA_gb.mdin), then run again using the
"-use-mdins" file.

Note that GB has not been parametrized or tested with dielectric constants
besides 1.0 and 80.0 (or 78.5). Technically, the 'internal' dielectric
constant in GB really should be 1.0 --- it corresponds to the dielectric of
vacuum in the actual GB equation (the internal dielectric constant of the
protein actually cancels out in the deltaG expression).

The argument for modifying the internal dielectric constant as a model of
the dielectric of the interior of the protein is dubious, though not
indefensible. Trying to use any of the Amber GB models for anything except
water is probably flat-out wrong. PB is better suited for these types of

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Received on Thu Jul 04 2013 - 08:30:04 PDT
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