If you want to run MMPBSA in parallel, you need to use the MMPBSA.MPI
executable, not MMPBSA. Also, try running GB and PB calculations in
separate steps to make sure you get a FINAL_RESULTS_MMPBSA.dat for each
step that completes successfully.
HTH,
Jason
On Thu, Dec 15, 2011 at 2:00 AM, Rajesh Singh <rajeshsingh2008.gmail.com>wrote:
> 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
>
>
> **********************************************************************************************************************
> _______________________________________________
> 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
Received on Thu Dec 15 2011 - 05:00:04 PST
