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
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Received on Tue Jun 04 2013 - 15:00:02 PDT
