Dear Dr. Jason,
Thank you for the help. It is running well now.
Best Regards,
kamlesh
On Mon, Jul 5, 2010 at 12:04 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> Your problem has to do with the fact that you're trying to use amber10, and
> the PB input file has changed a lot since that version. We do run a check
> for whether or not you're using amber10, but the easiest way we had of
> doing
> that was to simply test to see if amber10 appeared in your sander path.
> However, yours is amber_10, so it's not recognized and as such is using the
> amber11 input file.
>
> You'll have to make a very minor change to MMPBSA.py.MPI and MMPBSA.py.
> Search for the phrase "uncomment this for amber10 or older for amber pbsa
> only!". The phrase "uncomment this" should be enough to uniquely identify
> the line. The lines should look like
>
> if utils.digit(INPUT[0],1) == 1:
> if not use_mdins and master:
> utils.pbmdin(INPUT)
> # utils.pbmdin_old(INPUT) # uncomment this for amber10 or older for
> amber pbsa only!
> elif use_mdins:
>
> In python, # represents the comment, so comment out utils.pbmdin(INPUT) and
> uncomment utils.pbmdin_old(INPUT) ... Then don't forget to run the tests
> so
> that you can make sure it's actually working.
>
> Hope this helps,
> Jason
>
> On Sun, Jul 4, 2010 at 9:56 PM, kamlesh sahu <kamleshsemail.gmail.com
> >wrote:
>
> > Dear Amber users,
> >
> > I am running MMPBSA.py.MPI using the following command -
> >
> > >mpirun -np 4 ~/src/Xtruct/trunk/amber_10_install/bin/MMPBSA.py.MPI -O -i
> > mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp solvated_complex.prmtop -cp
> > complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
> >
> > Everytime (with zinc ions, without zn ions, with/without crystallographic
> > waters), I get the following error (this error occurs even when i run
> > MMPBSA.py with input files provided in tutorial 3.2) ---->
> >
> > MMPBSA.py.MPI being run on 4 processors
> > ptraj found! Using
> /home/ksahu/src/Xtruct/trunk/amber_10_install/bin/ptraj
> > sander found! Using
> > /home/ksahu/src/Xtruct/trunk/amber_10_install/bin/sander
> > Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
> modified
> > Bondi radii (mbondi)
> >
> > Preparing trajectories with ptraj...
> > 21 frames were read in and processed by ptraj for use in calculation.
> >
> > Starting calculations
> >
> > Starting gb calculation...
> >
> > calculating ligand contribution...
> > calculating receptor contribution...
> > calculating complex contribution...
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > Starting pb calculation...
> >
> > calculating ligand contribution...
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > calculating receptor contribution...
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> > calculating complex contribution...
> > Cannot match namelist object name ipb
> > namelist read: missplaced = sign
> > Cannot match namelist object name inp
> > namelist read: missplaced = sign
> >
> > Calculations complete. Writing output file(s)...
> > Error: No potential terms in sander output! Check output files.
> > NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> > --clean to erase these files.
> >
> >
> >
> >
> > The FINAL_RESULTS_MMPBSA.dat file reads -
> >
> > | Run on Fri Jul 2 10:22:39 JST 2010
> >
> > |Input file:
> > |--------------------------------------------------------------
> > |Input file for running PB and GB
> > |&general
> > | endframe=50, verbose=1,
> > |# entropy=1,
> > |/
> > |&gb
> > | igb=2, saltcon=0.100,
> > | gbsa=1
> > |/
> > |&pb
> > | istrng=0.100,
> > |/
> > |--------------------------------------------------------------
> > |Complex topology file: complex.prmtop
> > |Receptor topology file: receptor.prmtop
> > |Ligand topology file: ligand.prmtop
> > |Initial mdcrd(s): equil.mdcrd
> > |
> > |Best guess for receptor mask: ":1-423:425-599"
> > |Best guess for ligand mask: ":424"
> > |Ligand residue name is "SAM"
> > |
> > |Calculations performed using 25 frames.
> > |Poisson Boltzmann calculations performed using internal PBSA solver in
> > sander.
> > |
> > |All units are reported in kcal/mole.
> >
> >
> > Is this a prolem with installation or something ?
> >
> > Thank you
> > Best Regards,
> >
> >
> -------------------------------------------------------------------------------
> > -------------------------------------------------------------------------
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN
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Received on Sun Jul 04 2010 - 23:30:03 PDT
