igb=8 works fine for me with MMPBSA.py Version=12.0. You can look at the
igb.8.dat file. I am not sure what happens with your version.
Best
Hai
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
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>
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- application/octet-stream attachment: igb.8.dat
Received on Tue Jun 04 2013 - 17:30:02 PDT
