MM/PB(GB)SA is known to be largely unreliable for absolute binding free
energies. Are you comparing a range of ligands with the same receptor (or
a range of receptors with the same ligand)? Or are you trying to get an
absolute free energy?
Hopefully both methods give you the correct trend in binding free energies,
but to expect both to give you similar absolute binding free energies is
expecting too much, in my opinion. (Notice I said similar -- that says
nothing about them being 'right'.)
MM/PBSA is most useful for determining differences in DELTA G of binding
between different ligands, since a large number of the errors in the
approximations are present for each system and cancel out.
HTH,
Jason
On Mon, Jul 23, 2012 at 7:09 PM, sudipta <sudipta.mml.gmail.com> wrote:
> Hi Ray,
>
> Including the radiopt=0 and inp=1 in the PB section, the script finishes
> without any error. Thank you very much for helpful suggestion. However, the
> values obtained from these two methods are markedly different and I can't
> able rely on this calculation. Can you please suggest how do I get
> converged result from both methods.
>
> Looking forward to hear from you soon.
>
> Thanks again
> Sudipta
>
> On Mon, Jul 23, 2012 at 3:09 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
> > Sudipta,
> >
> > If you have modeled any nonstandard residue, please use radipt=0 only.
> This
> > limits your choice of nonpolar solvation treatment to inp=1 only, i.e.
> the
> > simple SA approach. We will revisit this issue in the next release to
> allow
> > people use inp=2 with nonstandard residues whether PB is requested or
> not.
> >
> > All the best,
> > Ray
> >
> > On Mon, Jul 23, 2012 at 3:01 PM, sudipta <sudipta.mml.gmail.com> wrote:
> >
> > > HI Ray,
> > >
> > > My system contain a protein-DNA complex. But the protein is a zinc
> finger
> > > protein and I have modeled ZN atom as a nonstandard residue. So, what
> > shall
> > > I do next?
> > >
> > > Thanks
> > > Sudipta
> > >
> > > On Mon, Jul 23, 2012 at 2:54 PM, Ray Luo, Ph.D. <ray.luo.uci.edu>
> wrote:
> > >
> > > > You are using radiopt=1 for the inp=2 option of nonpolar solvation
> free
> > > > energy calculation. Do you have any ligand or other nonstandard
> > residues
> > > in
> > > > the system?
> > > >
> > > > All the best,
> > > > Ray
> > > >
> > > > On Mon, Jul 23, 2012 at 2:38 PM, sudipta <sudipta.mml.gmail.com>
> > wrote:
> > > >
> > > > > Hi Jason,
> > > > >
> > > > > Thank you very much for your reply.
> > > > >
> > > > > Please find the attached file. This file contains all
> > > _MMPBSA_*_pb.mdout
> > > > > files. Feel free to contact me if you need any further information
> > from
> > > > my
> > > > > side.
> > > > >
> > > > > Thanks again
> > > > > Sudipta
> > > > >
> > > > > On Mon, Jul 23, 2012 at 2:32 PM, Jason Swails <
> > jason.swails.gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Hi Sudipta,
> > > > > >
> > > > > > This error message means that the PB energy calculation failed,
> > which
> > > > is
> > > > > > actually an error within PBSA. It would be more helpful to
> include
> > > the
> > > > > > _MMPBSA_*_pb.mdout files, since any error messages may be hidden
> > > inside
> > > > > > there.
> > > > > >
> > > > > > All the best,
> > > > > > Jason
> > > > > >
> > > > > > On Mon, Jul 23, 2012 at 4:03 PM, sudipta <sudipta.mml.gmail.com>
> > > > wrote:
> > > > > >
> > > > > > > Hi Jason and Amber users,
> > > > > > >
> > > > > > > I have been facing a strange problem with PB calculation for a
> > > > > > protein-DNA
> > > > > > > system from the last week. The error looks like
> > > > > > >
> > > > > > > /home/sudipta/Downloads/amber12/bin/mmpbsa_py_energy failed
> > with
> > > > > prmtop
> > > > > > >
> > > > > > > The script, MMPBSA.py.MPI has finished GB calculation for my
> > system
> > > > > > without
> > > > > > > any error. Moreover, the tutorial files finish without any
> > error.
> > > > > Please
> > > > > > > find the attached two final output files of those two
> > calculations.
> > > > It
> > > > > > > really puzzles me why PB calculation is not finishing properly
> > for
> > > my
> > > > > > > system. I don't get any fruitful error message except the above
> > > one.
> > > > By
> > > > > > the
> > > > > > > way, I am using only AmberTools12 and the OS is Ubuntu 10.4.
> > > > > > >
> > > > > > > Looking forward to hear from you soon.
> > > > > > >
> > > > > > > Thanks in advance
> > > > > > > Sudipta
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Jason M. Swails
> > > > > > Quantum Theory Project,
> > > > > > University of Florida
> > > > > > Ph.D. Candidate
> > > > > > 352-392-4032
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > > _______________________________________________
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> > > > >
> > > > >
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> > > >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 23 2012 - 16:30:03 PDT
