Try using the AmberTools 1.5 version instead of the previous version. In
AmberTools 1.5, the correct name of the executable is MMPBSA.MPI, not
MMPBSA.py.MPI. This may be causing your issues.
Try replacing MMPBSA.py.MPI with MMPBSA.MPI and see if that helps.
If you do not have MMPBSA and MMPBSA.MPI in $AMBERHOME/bin, then AmberTools
1.5 wasn't installed properly. If you do, then delete MMPBSA.py.MPI and
MMPBSA.py from $AMBERHOME/bin to avoid any confusion. I thought this was
done automatically, but I must have missed that.
HTH,
Jason
On Fri, Jul 22, 2011 at 6:15 PM, Seungyeul Yoo <Seungyeul.Yoo.mssm.edu>wrote:
> Hi all,
>
> I'm using MMPBSA.py script to calculate binding affinity.
>
> I use the same topology files for -sp and -cp since I already stripped all
> the water molecules and ions using trajout command in ptraj.
>
> The input file for running GB and PB is following:
>
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> &general
> verbose=2, entropy=0, strip_mdcrd=1
> startframe=60, endframe=6000, interval=60
> /
> &decomp
> idecomp=2, dec_verbose=3
> print_res="21-33;43-48;62-83;90-110;138-149;155-161;290-292"
> /
> &gb
> igb=5, saltcon=0.150
> /
> &pb
> istrng=0.150
> /
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Then I submit this input file in PBS server using following commands:
>
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/intel/lib/intel64
> export AMBERHOME=/share/apps/amber11
> export
> PYTHONPATH=/share/apps/python2.6/lib/python2.6/site-packages\:$PYTHONPATH
> MMPBSA="/share/apps/amber11/bin/MMPBSA.py.MPI"
> PYTHON="/share/apps/python27/bin/python2.7"
>
> cd $PBS_O_WORKDIR
>
> SUB="mpirun -np 4 $PYTHON $MMPBSA -O -i decomp_lig.in -o decomp_lig.dat
> -sp ../Analysis/plk2_168_com.top -cp ../Analysis/plk2_168_com.top -rp
> ../Analysis/plk2_168_rec.top -lp ../Analysis/plk2_168_lig.top -y
> ../Analysis/plk2_168_dck_now.trj -do plk2_168_decomp.dat"
> echo $SUB
> $SUB
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> The command finished with error having log of
>
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> mpirun -np 4 /share/apps/python27/bin/python2.7
> /share/apps/amber11/bin/MMPBSA.py.MPI -O -i decomp_lig.in -o
> decomp_lig.dat -sp ../Analysis/plk2_168_com.top -cp
> ../Analysis/plk2_168_com.top -rp ../Analysis/plk2_168_rec.top -lp
> ../Analysis/plk2_168_lig.top -y ../Analysis/plk2_168_dck_now.trj -do
> plk2_168_decomp.dat
> MMPBSA.py.MPI being run on 4 processors
> ptraj found! Using /share/apps/amber11/exe/ptraj
> sander found! Using /share/apps/amber11/exe/sander
>
> Preparing trajectories with ptraj...
> 100 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...
> Starting pb calculation...
>
> calculating ligand contribution...
> calculating receptor contribution...
> calculating complex contribution...
>
> Calculations complete. Writing output file(s)...
> Traceback (most recent call last):
> File "/share/apps/amber11/bin/MMPBSA.py.MPI", line 1571, in <module>
> decompout, idecomp, dec_verbose, ligstart, decomprun, surften,
> cavity_surften, temp)
> File "/share/apps/amber11/bin/utils.py", line 4647, in PrintFinalResults
> '',finaloutput,debug,numframes,sander_apbs,one_trajectory,verbose)
> File "/share/apps/amber11/bin/utils.py", line 2248, in pboutput
> bonddif[x] = bonddif[x] - bond[x]
> IndexError: list index out of range
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Therefore in the output file, only GB information is printed and no PB
> results.
>
> Strangely, I have another system with point mutation and run the MMPBSA.py
> without error.
>
> I checked the version of the versions of all packages such as "AMBERTOOLS
> 1.5" and they were all updated.
>
> Can I have any advices where I need to look at to solve this problem?
>
> Thanks,
>
> Seungyeul Yoo
>
> _______________________________________________
> 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
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Received on Fri Jul 22 2011 - 19:00:02 PDT
