Hi
Thank you Jason and Ray for your helpful suggestion. Yes, I want to see
some relative binding free energy differences for a variety of protein-DNA
systems. In that sense, I hope it will work.
Could you suggest a method by which I can calculate reliable absolute free
energy of binding of a protein-DNA system. The system is huge. It contains
around 5000 atoms (total number of atoms of the protein-DNA complex). So is
it possible to sampling of this huge system by any non-equilibrium method
(such as free energy perturbation, umbrella sampling, metadynamics etc.).
In this regard if you have any suggestion, please share it.
Thanks in advance
Sudipta
On Mon, Jul 23, 2012 at 4:42 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Indeed, the inp=1 and inp=2 are very different ... However, most people
> have been using inp=1, i.e. the simple SA approach, for their mmpbsa
> calculations in the past and are happy with it, at least for relative
> binding free energies.
>
> All the best,
> Ray
>
> On Mon, Jul 23, 2012 at 4:09 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
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Received on Mon Jul 23 2012 - 18:00:02 PDT
