Hi Jason,
I do have MMPBSA and MMPBSA.MPI in $AMBERHOME/bin folder.
And MMPBSA.MPI contains only following lines
------------------------------------------------------------------------------------------------------------------------------
#!/bin/sh
if [ -z $AMBERHOME ]; then
echo "Error: AMBERHOME must be set for MMPBSA!"
exit 1
fi
if [ ! -f $AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI ]; then
echo "Error: Can't find MMPBSA.py.MPI! Re-install MMPBSA.py in parallel."
exit 1
fi
$AMBERHOME/bin/python $AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI $*
------------------------------------------------------------------------------------------------------------------------------
Is this what you think I need to run instead of MMPBSA.py.MPI?
When I used this MMPBSA.MPI, the job was again failed with error message.
------------------------------------------------------------------------------------------------------------------------------
Error: Can't find MMPBSA.py.MPI! Re-install MMPBSA.py in parallel.
Error: Can't find MMPBSA.py.MPI! Re-install MMPBSA.py in parallel.
Error: Can't find MMPBSA.py.MPI! Re-install MMPBSA.py in parallel.
Error: Can't find MMPBSA.py.MPI! Re-install MMPBSA.py in parallel.
------------------------------------------------------------------------------------------------------------------------------
Since there is no MMPBSA.py.MPI file in the path of $AMBERHOME/AmberTools/src/mmpbsa_py/ .
Is the MMPBSA.py.MPI called in MMPBSA.MPI different from MMPBSA.py.MPI?
If so, I would ask our computer administrator to reinstall MMPBSA.py in the path.
If there is anything to be careful here please let me know.
Thank you so much for your help.
Seungyeul Yoo
On Jul 22, 2011, at 9:30 PM, Jason Swails wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Jul 22 2011 - 23:30:02 PDT
