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
Received on Tue Jun 04 2013 - 18:00:03 PDT
