In that case, you probably need to update your Amber installation.
If you re-run configure, it should apply all of the updates (then don't
forget to rebuild your installation).
One of the bug fixes prevents error messages from being suppressed (but
doesn't actually fix the errors).
Good luck,
Jason
On Wed, Mar 27, 2013 at 1:46 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>wrote:
> Thank you
>
> This is only what is in the _MMPBSA_complex_pb.mdout.0. file. I don't see
> an error msg there.
>
> Reading parm file (../complex.prmtop)
> title:
> default_name
>
> mm_options: e_debug=3
> mm_options: ipb=2
> mm_options: inp=2
> mm_options: epsin=1.000000
> mm_options: epsout=80.000000
> mm_options: smoothopt=1
> mm_options: istrng=100.000000
> mm_options: radiopt=1
> mm_options: dprob=1.400000
> mm_options: iprob=2.000000
> mm_options: npbopt=0
> mm_options: solvopt=1
> mm_options: accept=0.001000
> mm_options: maxitn=1000
> mm_options: fillratio=4.000000
> mm_options: space=0.500000
> mm_options: nfocus=2
> mm_options: fscale=8
> mm_options: bcopt=5
> mm_options: eneopt=2
> mm_options: cutnb=0.000000
> mm_options: sprob=0.557000
> mm_options: cavity_surften=0.037800
> mm_options: cavity_offset=-0.569200
> Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
>
> Processing frame 1
> iter Total bad vdW elect nonpolar EPB
> frms
>
>
>
> On Wed, Mar 27, 2013 at 11:48 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > The error message will be found in _MMPBSA_complex_pb.mdout.0.
> >
> > If you google the error message you get, it should take you to previous
> > discussions on the mailing list where people have asked that question and
> > received answers.
> >
> > Good luck,
> > Jason
> >
> > On Wed, Mar 27, 2013 at 12:08 PM, Chinthaka Ratnaweera <
> cnr88.msstate.edu
> > >wrote:
> >
> > > Hi
> > > I am getting following error when calculating the MMPBSA energies with
> > > MMPBSA.py. But GBSA works fine. Error msg and input files are paste
> > below.
> > > Thank you in advanced.
> > >
> > > Reading command-line arguments and input files...
> > > Loading and checking parameter files for compatibility...
> > > mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
> > > cpptraj found! Using /usr/local/amber12/bin/cpptraj
> > > Preparing trajectories for simulation...
> > > 50 frames were processed by cpptraj for use in calculation.
> > >
> > > Beginning PB calculations with /usr/local/amber12/bin/mmpbsa_py_energy
> > > calculating complex contribution...
> > > CalcError: /usr/local/amber12/bin/mmpbsa_py_energy failed with prmtop
> > > ../complex.prmtop!
> > >
> > >
> > > Exiting. All files have been retained.
> > >
> > > ...................
> > >
> > > input file
> > >
> > > input file for running PB and GB in serial
> > > &general
> > > endframe=50, keep_files=2,
> > > /
> > > &gb
> > > igb=2, saltcon=0.100,
> > > /
> > > &pb
> > > istrng=0.100,
> > > /
> > >
> > >
> > > --
> > > Chinthaka Nadun Ratnaweera
> > > Mississippi State University
> > > 310 Presidents Circle
> > > Starkville, MS 39762
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
> _______________________________________________
> 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
Received on Wed Mar 27 2013 - 12:30:03 PDT
