Dear All,
I wanna calculate *Per-residue free energy decomposition* and for that
MMPBSA.py job was performed on parallel, in a quad-core machine. But
unfortunaltely I got a *sander error during PB calculations* (see below).
Could any help me about the reason of the failure of this job.
Moreover, I didn't obtained any files named "*FINAL_RESULTS_MMPBSA.dat*"
and "*decomp_output_file*". But rather am having _MMPBSA_complex_gb.mdout
file. As my GB calculations were complete, is there any chance to prepare
FINAL_RESULTS_MMPBSA.dat result file from _MMPBSA_complex_gb.mdout.
Please suggest any command/tutorial.
Thanks and regards
Rajesh Singh <rajeshsingh2008.gmail.com>
NIPER, India
**********************************************************************************************************************
*mmpbsa_decomp.in*
Per-residue GB and PB decomposition
&general
endframe=2000, verbose=1,
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1, print_res="1-279"
dec_verbose=1,
/
**********************************************************************************************************************
**********************************************************************************************************************
tail *_MMPBSA_complex_pb.mdout *
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
trajectory generated by
ptraj
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by
ptraj
minimizing coord set # 1
SA Bomb in sa_arc()3: Allocates aborted 0 0
1 0 0
[root.localhost MMPBSA]# tail _MMPBSA_complex_pb.mdout
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by
ptraj
minimizing coord set # 1
SA Bomb in sa_arc()3: Allocates aborted 0 0
1 0 0
**********************************************************************************************************************
**********************************************************************************************************************
*[root.localhost MMPBSA]# mpirun -np 8 $AMBERHOME/bin/MMPBSA -O -i
mmpbsa_decomp.in -o FINAL_RESULTS_MMPBSA.dat -sp tmc4_sol.prmtop -cp
tmc4.prmtop -rp tmcr.prmtop -lp tak.prmtop -y prod.mdcrd -do
decomp_output_file
*Reading command-line arguments and input files...
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Reading command-line arguments and input files...
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
Reading command-line arguments and input files...
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Reading command-line arguments and input files...
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
ptraj found! Using /opt/amber11/bin/ptraj
sander found! Using /opt/amber11/bin/sander for GB calculations
sander found! Using /opt/amber11/bin/sander for PB calculations
ptraj found! Using /opt/amber11/bin/ptraj
sander found! Using /opt/amber11/bin/sander for GB calculations
sander found! Using /opt/amber11/bin/sander for PB calculations
ptraj found! Using /opt/amber11/bin/ptraj
sander found! Using /opt/amber11/bin/sander for GB calculations
sander found! Using /opt/amber11/bin/sander for PB calculations
Preparing trajectories for simulation...
Preparing trajectories for simulation...
Preparing trajectories for simulation...
ptraj found! Using /opt/amber11/bin/ptraj
sander found! Using /opt/amber11/bin/sander for GB calculations
sander found! Using /opt/amber11/bin/sander for PB calculations
ptraj found! Using /opt/amber11/bin/ptraj
sander found! Using /opt/amber11/bin/sander for GB calculations
sander found! Using /opt/amber11/bin/sander for PB calculations
Preparing trajectories for simulation...
ptraj found! Using /opt/amber11/bin/ptraj
sander found! Using /opt/amber11/bin/sander for GB calculations
sander found! Using /opt/amber11/bin/sander for PB calculations
Preparing trajectories for simulation...
Preparing trajectories for simulation...
ptraj found! Using /opt/amber11/bin/ptraj
sander found! Using /opt/amber11/bin/sander for GB calculations
sander found! Using /opt/amber11/bin/sander for PB calculations
Preparing trajectories for simulation...
ptraj found! Using /opt/amber11/bin/ptraj
sander found! Using /opt/amber11/bin/sander for GB calculations
sander found! Using /opt/amber11/bin/sander for PB calculations
Preparing trajectories for simulation...
2000 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
2000 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
2000 frames were read in and processed by ptraj for use in calculation.
2000 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
Beginning GB calculations with sander...
calculating complex contribution...
2000 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
2000 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
2000 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
2000 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating ligand contribution...
calculating ligand contribution...
calculating ligand contribution...
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
MMPBSA.py --clean
/opt/amber11/exe/MMPBSA.py: line 17: VERSION: command not found
/opt/amber11/exe/MMPBSA.py: line 44: try:: command not found
/opt/amber11/exe/MMPBSA.py: line 45: except:: command not found
/opt/amber11/exe/MMPBSA.py: line 46: print: command not found
/opt/amber11/exe/MMPBSA.py: line 47: syntax error near unexpected token `1'
/opt/amber11/exe/MMPBSA.py: line 47: ` quit(1)'
[1]+ Exit 1 /usr/local/bin/mpirun -np 8
$AMBERHOME/bin/MMPBSA -O -i mmpbsa_decomp.in -o FINAL_RESULTS_MMPBSA.dat
-sp tmc4_sol.prmtop -cp tmc4.prmtop -rp tmcr.prmtop -lp tak.prmtop -y
prod.mdcrd -do decomp_output_file
You have new mail in /var/spool/mail/root
**********************************************************************************************************************
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Received on Wed Dec 14 2011 - 23:30:02 PST
