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,
>
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Jul 04 2010 - 20:30:03 PDT
