Dear Amber Users,
I am trying to run MMPBSA with an intention to calculate binding free
energy of a protein-protein complex in amber v.14. The input file was :
&general
startframe=1, endframe=500, verbose=1, search_path=1
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
And the script was :
#! /bin/bash
#$ -cwd
#$ -S /bin/bash
#$ -e err.$JOB_ID.$JOB_NAME
#$ -o out.$JOB_ID.$JOB_NAME
#$ -pe mpi 16
source /etc/profile
#export AMBERHOME=/opt/amber14/amber14/bin/
/opt/amber14/amber14/bin/MMPBSA.py -O -i mmpbsa.in -o complex-mmpbsa.dat
-sp complex-wat.prmtop -cp complex.prmtop -rp receptor-only.prmtop -lp
ligand-only.prmtop -y *.mdcrd > process.log 2>&1
And I have encountered following error:
File "/opt/amber14/amber14/bin/MMPBSA.py", line 95, in <module>
app.file_setup()
File "/opt/amber14/amber14/bin/MMPBSA_mods/main.py", line 135, in
file_setup
external_progs = find_progs(self.INPUT)
File "/opt/amber14/amber14/bin/MMPBSA_mods/findprogs.py", line 41, in
find_progs
raise MMPBSA_Error('Could not find necessary program [%s]' % prog)
MMPBSA_Error: Could not find necessary program [mmpbsa_py_energy]
Exiting. All files have been retained.
Please help me understand the error message, reason being when i cross
checked the bin directory I could locate mmpbsa_py_energy. Please let me
know where I am going wrong? Thanks for your time!
--
Regards,
Pallavi Mohanty
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Received on Wed Jan 06 2016 - 00:00:05 PST
