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
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Received on Fri Jul 22 2011 - 15:30:03 PDT
