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
> > > > > >
> > > > > > _______________________________________________
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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
