Hello Amber Gurus,
i am unable to run MMPBSA.py script a set of Amber MD trajectory structures
as the job dies with the following set of errors:
=============== error output ===========
/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
app.run_mmpbsa()
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
218, in run_mmpbsa
app.run_mmpbsa()
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
218, in run_mmpbsa
app.run_mmpbsa()
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 79, in run
self.calc_list.run(rank, self.stdout)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 79, in run
self.calc_list.run(rank, self.stdout)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 79, in run
app.run_mmpbsa()
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 79, in run
app.run_mmpbsa()
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 79, in run
app.run_mmpbsa()
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
218, in run_mmpbsa
app.run_mmpbsa()
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
self.calc_list.run(rank, self.stdout)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 79, in run
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 79, in run
app.run_mmpbsa()
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 415, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError: /home/shashi/amber/bin/sander failed with prmtop
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
Error occured on rank 1.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 415, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
calc.run(rank, stdout=stdout, stderr=stderr)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 415, in run
CalcError: /home/shashi/amber/bin/sander failed with prmtop
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
Error occured on rank 5.
Exiting. All files have been retained.
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError: /home/shashi/amber/bin/sander failed with prmtop
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
Error occured on rank 3.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 415, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError: /home/shashi/amber/bin/sander failed with prmtop
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
Error occured on rank 0.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 415, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError: /home/shashi/amber/bin/sander failed with prmtop
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
Error occured on rank 7.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 415, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError: /home/shashi/amber/bin/sander failed with prmtop
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
Error occured on rank 4.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 415, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError: /home/shashi/amber/bin/sander failed with prmtop
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
Error occured on rank 2.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
line 415, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError: /home/shashi/amber/bin/sander failed with prmtop
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
Error occured on rank 6.
Exiting. All files have been retained.
===============================================================================================
the input file used looks like this:
========== input file ==================
&general
startframe=1, endframe=99999, interval=1, verbose=2, keep_files=1,
ligand_mask=":199",
/
&pb
istrng=0.15, fillratio=4.0,
/
&decomp
idecomp=2, dec_verbose=3
/
========= end of input file ===================
the command used (after setting all the environment variables like
AMBERHOME, PATH and LD_LIBRARY_PATH) was as follows:
/home/snr49/source/amber/bin/mpirun -np 8 MMPBSA.py.MPI -O -i
/home/shashi/HIV_AMBER/INDIA/SSSS/MMPBSA/mmpbsa_input -cp
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop -rp
/home/shashi/HIV_AMBER/INDIA/1QBT_proteinonly.prmtop -lp
/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBTLIGAND.prmtop -eo
ENERGY_traj1_SSSS.csv -y 1QBT_dmp_SSSS_complex_collection1_NoSOLVENT.netcdf
-o FINAL_SSSS_traj1_Results.dat -do FINAL_SSSS_traj1_DECOMP_MMPBSA.dat
==========================
i also separately executed (successfully) a sander run for minimizing one
of the trajectory structures with the parm topology file
"/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop". Hence
I am a little puzzled as to why the program would complain about the
failure of sander with the topology file. I may also add that earlier, I
had successfully run MMGBSA calculations on the same trajectory.
thanks for help in resolving this issue,
Shashi Rao
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Wed Sep 24 2014 - 08:30:03 PDT
