There are 3 (!) implementations of the GB models in Amber. Hai pointed out
the first one. The other two are in nab
($AMBERHOME/AmberTools/src/sff/eff.c) and pmemd
($AMBERHOME/src/pmemd/src/gb_ene.F90). The sander source code contains all
of the details for doing GB with multiscale models (i.e., with QM/MM),
while the pmemd source code is simpler and cleaner and the nab source code
is in C (if you are more familiar with that language). The MMPBSA.py code
simply uses the GB implementations in nab and sander for its functionality.
But I agee with Hai -- there are other places to learn about GB. The code
will make *much* more sense after reading the manual and GB papers.
HTH,
Jason
On Wed, Sep 23, 2015 at 2:26 AM, Abhilash J <md.scfbio.gmail.com> wrote:
> Hi!
>
> Thanks. I will check it out.
>
> Regards
>
> Abhilash
>
> On Wed, Sep 23, 2015 at 11:02 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > On Wed, Sep 23, 2015 at 1:14 AM, Abhilash J <md.scfbio.gmail.com> wrote:
> >
> > > Hi!
> > >
> > > I have done MMGBSA and MMPBSA calculations using AMBER.
> > > I am interested in understanding implementation of MMGBSA in AMBER
> > > package.
> > > From where can i get information regarding this like any published
> > > paper
> >
> >
> > The 1st place you should look is amber15 manual:
> > http://ambermd.org/doc12/Amber15.pdf
> >
> > check "The Generalized Born/Surface Area Mode" chapter. There are lots of
> > papers there.
> >
> >
> > > or code that i can read to gain the insight in the working of GB
> > > calculations in AMBER.
> > >
> > >
> > You can check GB code in $AMBERHOME/AmberTools/src/sander/egb.F90
> >
> > For mmpbsa interface (Python), you can check its implementation
> > in AmberTools/src/mmpbsa_py/ folder.
> >
> > Hope this help
> >
> > Hai
> >
> >
> > >
> > >
> > > Regards
> > >
> > > Abhilash
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 23 2015 - 07:00:03 PDT
