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From: Rajesh Singh <rajeshsingh2008.gmail.com>

Date: Thu, 15 Dec 2011 12:12:04 +0530

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>

**********************************************************************************************************************

*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

Received on Wed Dec 14 2011 - 23:00:03 PST

Date: Thu, 15 Dec 2011 12:12:04 +0530

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>

**********************************************************************************************************************

*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

Received on Wed Dec 14 2011 - 23:00:03 PST

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