Dear Hai and Jason,
Thanks for the prompt reply. After applying the latest bug fix,
login1$ $AMBERHOME/update_amber --update
login1$ $AMBERHOME/update_amber --version
Version is reported as <version>.<patches applied>
AmberTools version *13.09*
Amber version *12.18*
Using *igb==8 * in AmberTools13 & Amber12 with the same Ras-Raf testing
files, we still suffer the same error message (but there are a couple more
lines of error messages, *bolded*) :
(no issue in using *igb==7*)
MMPBSA.py -O -i mmpbsa.in -o igb.8.dat -sp sol.top -cp complex.top -rp
receptor.top -lp ligand.top -y test.mdcrd
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using $AMBERHOME/bin/mmpbsa_py_energy
cpptraj found! Using $AMBERHOME/bin/cpptraj
Preparing trajectories for simulation...
2 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with $AMBERHOME/bin/mmpbsa_py_energy
calculating complex contribution...
*
File "$AMBERHOME/bin/MMPBSA.py", line 91, in ?
app.run_mmpbsa()
File "$AMBERHOME/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "$AMBERHOME/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "$AMBERHOME/bin/MMPBSA_mods/calculation.py", line 155, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,*
CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop complex.top!
Exiting. All files have been retained.
python2.4:
/home1/0000/build/admin/rpms/lonestar42/BUILD/mvapich2-1.6/src/mpid/ch3/channels/common/src/memory/mem_hooks.c:160:
mvapich2_mfin: Assertion `1 == mem_hook_init' failed.
run.pbs.igb.8: line 3: 4246 Aborted MMPBSA.py -O -i
mmpbsa.in -o igb.${X}.dat -sp sol.top -cp complex.top -rp receptor.top -lp
ligand.top -y test.mdcrd
May we know if we still have to call sander for igb==8 in AmberTool13?
Or is it due to our ignorance? Or there is other issue? Thanks.
Cheers,
Henry
On Tue, Jun 4, 2013 at 7:34 PM, Jason Swails <jason.swails.gmail.com> wrote:
> I found the error and will be issuing a fix shortly.
>
> Basically, the problem is that igb==8 still triggers writing a sander input
> file, even though the NAB program can still handle it. I'm not sure how
> that slipped through, but it's an easy fix.
>
> After applying the fix, everything seems to work well:
>
> $ MMPBSA.py -O -i mmpbsa.in -o igb.8.dat -sp sol.top -cp complex.top -rp
> receptor.top -lp ligand.top -y test.mdcrd.gz
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /home/swails/build_amber/amber/bin/mmpbsa_py_energy
> cpptraj found! Using /home/swails/build_amber/amber/bin/cpptraj
> Preparing trajectories for simulation...
> 2 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with
> /home/swails/build_amber/amber/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Timing:
> Total setup time: 3.238 sec.
> Creating trajectories with cpptraj: 10.067 sec.
> Total calculation time: 5.366 sec.
>
> Total GB calculation time: 5.366 sec.
>
> Statistics calculation & output writing: 0.001 sec.
> Total time taken: 18.681 sec.
>
>
> MMPBSA.py Finished! Thank you for using. Please cite us if you publish this
> work with this paper:
> Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke,
> H. and Roitberg, A. E.
> J. Chem. Theory Comput., 2012, 8 (9) pp 3314--3321
>
>
> Thanks for the report!
> Jason
>
>
> On Tue, Jun 4, 2013 at 5:44 PM, <psu4.uic.edu> wrote:
>
> > Dear Amber,
> >
> > After installed the new AmberTools 13, we tried our protein-ligand
> > system in different mmGBSA methods (igb=1,2,5,7,8). However, while
> > igb=1,2,5,7 run successfully, igb =8 always produces the following error
> > and mmGBSA/igb=8 will stop before producing *_gb.mdout, either in serial
> > (MMPBSA.py) or MPI (MMPBSA.py.MPI)
> >
> >
> > CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop
> > complex.top!
> >
> >
> > *a. *We use the following commands in parameter preparation to set
> > ff12SB, mbondi2 for igb=7 & 8 calculation.
> >
> > source leaprc.gaff
> >
> > source leaprc.ff12SB
> >
> > set default PBradii mbondi2
> >
> > *b. *Amber12 & AmberTools 13 were installed using the following
> > compilers:
> >
> > module load gcc/4.4.5
> >
> > module load mvapich2/1.6
> >
> > ./compile gnu (bug fix update to the newest)
> >
> > make install
> >
> > make test (everything passes test)
> >
> > ./compile gnu -mpi (bug fix update to the newest)
> >
> > make install
> >
> > make test (everything passes test)
> >
> > We eventually test igb=7 & igb=8 using Ras-Raf in
> > $AMBERHOME/amber12/AmberTools/test/mmpbsa_py/01_Generalized_Born. We
> > prepare Ras-Raf parameters with ff12SB and mbondi2 and re-run the
> > simulation and mmGBSA calculation. Again, igb=7 runs successfully in
> this
> > Ras-Raf system while igb=8 fails again with the same error message:
> > CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop
> complex.top!
> >
> > Herein we attached<
> > https://www.dropbox.com/s/nwkw3z9g7wer2uf/igb_7_8_test.tar.gz>our
> > Ras-Raf test files (MD files in igb_8_test/MD_test . Both _MMPBSA*
> > files are in igb_*_test/MMPBSA_temp . The file to run mmGBSA is
> > run.pbs.igb.X X=7 or 8). Could any guru kindly offer us any solution?
> Or
> > the error is due to our ignorance? Thanks.
> >
> > Cheers,
> > Henry
> > _______________________________________________
> > 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
>
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Received on Wed Jun 05 2013 - 11:30:03 PDT
