Sure, I've pasted them here.
I have _MMPBSA_ptraj1.out with _MMPBSA_ptraj1.out.[0-3]. _MMPBSA_ptraj2.out with _MMPBSA_ptraj2.out.[0-3] and _MMPBSA_ptraj3.out with _MMPBSA_ptraj3.out.[0-3]. There are also _MMPBSA_ptraj4.out, _MMPBSA_ptraj5.out and _MMPBSA_ptraj6.out.
Well, I have no idea which trajectory approach I'm using since I'm actually helping one of our users to get his MMPBSA job run on Ember(SGI Altix UV System) at NCSA.
Thanks
Ye
_MMPBSA_ptraj1.out:
--------------------------------------------------------------------------------------------------------------------------------------------
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "/u/ncsa/yefan/apps/amber11-gnu/bin/ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
LYS ILE ALA ALA LEU LYS GLN LYS ILE ALA
SER LEU LYS GLN GLU ILE ASP ALA LEU GLU
TYR GLU ASN ASP ALA LEU GLU GLN LYS ILE
ALA ALA LEU LYS GLN LYS ILE ALA SER LEU
LYS GLN GLU ILE ASP ALA LEU GLU TYR GLU
ASN ASP ALA LEU GLU GLN LYS ILE ALA ALA
LEU LYS GLN LYS ILE ALA SER LEU LYS GLN
GLU ILE ASP ALA LEU GLU TYR GLU ASN ASP
ALA LEU GLU GLN LYS ILE ARG ALA LEU LYS
ALA LYS ASN ALA HIE LEU LYS GLN GLU ILE
ALA ALA LEU GLU GLN GLU ILE ALA ALA LEU
GLU GLN LYS ILE ARG ALA LEU LYS ALA LYS
ASN ALA HIE LEU LYS GLN GLU ILE ALA ALA
LEU GLU GLN GLU ILE ALA ALA LEU GLU GLN
LYS ILE ARG ALA LEU LYS ALA LYS ASN ALA
HIE LEU LYS GLN GLU ILE ALA ALA LEU GLU
GLN GLU ILE ALA ALA LEU GLU GLN Na+ Na+
Na+ WAT WAT WAT WAT WAT WAT WAT WAT WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
...
WAT
PTRAJ: Processing input from file _MMPBSA_cenptraj.in
PTRAJ: trajin g1hexa_prod_comb 5251 5300 1
Checking coordinates: g1hexa_prod_comb
Rank: 0 Atoms: 41418 FrameSize: 1006483 TitleSize: 30 NumBox: 3 Seekable 1
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 38673 atoms
PTRAJ: center :1-56:223-278 mass origin
Mask [:1-56:223-278] represents 910 atoms
PTRAJ: image origin center
Mask [*] represents 2745 atoms
PTRAJ: center :1-168 mass origin
Mask [:1-168] represents 2745 atoms
PTRAJ: image origin center
Mask [*] represents 2745 atoms
PTRAJ: rms first mass :1-168
Mask [:1-168] represents 2745 atoms
PTRAJ: average _MMPBSA_avgcomplex.pdb pdb
Mask [*] represents 2745 atoms
PTRAJ: trajout _MMPBSA_complex.mdcrd nobox
g1hexa_prod_comb: 7420 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 50 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (g1hexa_prod_comb) is an AMBER trajectory (with box info) with 5300 sets (processing only 50)
OUTPUT COORDINATE FILE
File (_MMPBSA_complex.mdcrd) is an AMBER trajectory
ACTIONS
1> STRIP: 38673 atoms will be removed from trajectory: :169-13061
2> CENTER to origin via center of mass, atom selection follows :1-56
3> IMAGE by molecule to origin using the center of mass, atom selection * (All atoms are selected)
4> CENTER to origin via center of mass, atom selection follows * (All atoms are selected)
5> IMAGE by molecule to origin using the center of mass, atom selection * (All atoms are selected)
6> RMS to first frame using mass weighting
Atom selection follows * (All atoms are selected)
7> AVERAGE: dumping the average of the coordinates to file _MMPBSA_avgcomplex.pdb
start: 1 Stop [at final frame] Offset: 1
Atom selection * (All atoms are selected)
Output file information: File (_MMPBSA_avgcomplex.pdb) is a PDB file
Processing AMBER trajectory file g1hexa_prod_comb
........................ 75% 100%
PTRAJ: Successfully read in 50 sets and processed 50 sets.
Dumping accumulated results (if any)
--------------------------------------------------------------------------------------------------------------------------------------------
_MMPBSA_ptraj2.out:
--------------------------------------------------------------------------------------------------------------------------------------------
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "/u/ncsa/yefan/apps/amber11-gnu/bin/ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
LYS ILE ALA ALA LEU LYS GLN LYS ILE ALA
SER LEU LYS GLN GLU ILE ASP ALA LEU GLU
TYR GLU ASN ASP ALA LEU GLU GLN LYS ILE
ALA ALA LEU LYS GLN LYS ILE ALA SER LEU
LYS GLN GLU ILE ASP ALA LEU GLU TYR GLU
ASN ASP ALA LEU GLU GLN LYS ILE ALA ALA
LEU LYS GLN LYS ILE ALA SER LEU LYS GLN
GLU ILE ASP ALA LEU GLU TYR GLU ASN ASP
ALA LEU GLU GLN LYS ILE ARG ALA LEU LYS
ALA LYS ASN ALA HIE LEU LYS GLN GLU ILE
ALA ALA LEU GLU GLN GLU ILE ALA ALA LEU
GLU GLN LYS ILE ARG ALA LEU LYS ALA LYS
ASN ALA HIE LEU LYS GLN GLU ILE ALA ALA
LEU GLU GLN GLU ILE ALA ALA LEU GLU GLN
LYS ILE ARG ALA LEU LYS ALA LYS ASN ALA
HIE LEU LYS GLN GLU ILE ALA ALA LEU GLU
GLN GLU ILE ALA ALA LEU GLU GLN
PTRAJ: Processing input from file _MMPBSA_ligtraj.in
PTRAJ: trajin _MMPBSA_complex.mdcrd
Checking coordinates: _MMPBSA_complex.mdcrd
Rank: 0 Atoms: 2745 FrameSize: 66704 TitleSize: 30 NumBox: 0 Seekable 1
PTRAJ: strip :1-56:223-278
Mask [:1-56:223-278] represents 910 atoms
PTRAJ: trajout _MMPBSA_ligand.mdcrd nobox
_MMPBSA_complex.mdcrd: 50 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 50 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (_MMPBSA_complex.mdcrd) is an AMBER trajectory with 50 sets
OUTPUT COORDINATE FILE
File (_MMPBSA_ligand.mdcrd) is an AMBER trajectory
ACTIONS
1> STRIP: 910 atoms will be removed from trajectory: :1-56
Processing AMBER trajectory file _MMPBSA_complex.mdcrd
........................ 75% 100%
PTRAJ: Successfully read in 50 sets and processed 50 sets.
Dumping accumulated results (if any)
--------------------------------------------------------------------------------------------------------------------------------------------
_MMPBSA_ptraj3.out:
--------------------------------------------------------------------------------------------------------------------------------------------
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "/u/ncsa/yefan/apps/amber11-gnu/bin/ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
LYS ILE ALA ALA LEU LYS GLN LYS ILE ALA
SER LEU LYS GLN GLU ILE ASP ALA LEU GLU
TYR GLU ASN ASP ALA LEU GLU GLN LYS ILE
ALA ALA LEU LYS GLN LYS ILE ALA SER LEU
LYS GLN GLU ILE ASP ALA LEU GLU TYR GLU
ASN ASP ALA LEU GLU GLN LYS ILE ALA ALA
LEU LYS GLN LYS ILE ALA SER LEU LYS GLN
GLU ILE ASP ALA LEU GLU TYR GLU ASN ASP
ALA LEU GLU GLN LYS ILE ARG ALA LEU LYS
ALA LYS ASN ALA HIE LEU LYS GLN GLU ILE
ALA ALA LEU GLU GLN GLU ILE ALA ALA LEU
GLU GLN LYS ILE ARG ALA LEU LYS ALA LYS
ASN ALA HIE LEU LYS GLN GLU ILE ALA ALA
LEU GLU GLN GLU ILE ALA ALA LEU GLU GLN
LYS ILE ARG ALA LEU LYS ALA LYS ASN ALA
HIE LEU LYS GLN GLU ILE ALA ALA LEU GLU
GLN GLU ILE ALA ALA LEU GLU GLN
PTRAJ: Processing input from file _MMPBSA_rectraj.in
PTRAJ: trajin _MMPBSA_complex.mdcrd
Checking coordinates: _MMPBSA_complex.mdcrd
Rank: 0 Atoms: 2745 FrameSize: 66704 TitleSize: 30 NumBox: 0 Seekable 1
PTRAJ: strip :57-84:279-306
Mask [:57-84:279-306] represents 455 atoms
PTRAJ: trajout _MMPBSA_receptor.mdcrd nobox
_MMPBSA_complex.mdcrd: 50 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 50 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (_MMPBSA_complex.mdcrd) is an AMBER trajectory with 50 sets
OUTPUT COORDINATE FILE
File (_MMPBSA_receptor.mdcrd) is an AMBER trajectory
ACTIONS
1> STRIP: 455 atoms will be removed from trajectory: :57-84
Processing AMBER trajectory file _MMPBSA_complex.mdcrd
........................ 75% 100%
PTRAJ: Successfully read in 50 sets and processed 50 sets.
Dumping accumulated results (if any)
--------------------------------------------------------------------------------------------------------------------------------------------
On Jul 15, 2011, at 11:47 AM, Dwight McGee wrote:
> Hi,
>
> Can you attach or paste the following files _MMPBSA_ptraj1.out,
> _MMPBSA_ptraj2.out, _MMPBSA_ptraj3.out. Are you using a single trajectory or
> triple trajectory approach?
>
> On Fri, Jul 15, 2011 at 12:33 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>
>> Hi,
>>
>> I am still trying to debug the issue with MMPBSA.MPI. I could run the same
>> input files through MMPBSA successfully but always failed with parallel
>> version MMPBSA.MPI.
>>
>> Now, I have ruled out the previous suspicion that IOError was causing the
>> crash of calculation. The real reason is that a segmentation fault exception
>> was thrown during "calculating ligand contribution..." for GB calculation.
>> To be more specific: "mmpbsa_py_energy -O -i _MMPBSA_gb.mdin -o
>> _MMPBSA_ligand_gb.mdout.0 -p g1dimer_4hexa_nosolv.top -c
>> _MMPBSA_dummyligand.inpcrd.1 -y _MMPBSA_ligand.mdcrd.0 -r
>> _MMPBSA_.restrt_ligand.0 -pdb _MMPBSA_ligand.pdb" gives segmentation fault.
>> There is only 1 frame in _MMPBSA_ligand_gb.mdout.0. The same thing happens
>> to the other 3 processes.
>>
>> Another odd thing I've noticed was that "50 frames were read in and
>> processed by ptraj for use in calculation" was always showing up at
>> beginning of calculation for both parallel and serial run.
>>
>> For parallel run:
>> I checked
>> _MMPBSA_complex_gb.mdout.0 & _MMPBSA_receptor_gb.mdout.0 13
>> frames processed
>> _MMPBSA_complex_gb.mdout.1 & _MMPBSA_receptor_gb.mdout.1 13
>> frames processed
>> _MMPBSA_complex_gb.mdout.2 & _MMPBSA_receptor_gb.mdout.2 12
>> frames processed
>> _MMPBSA_complex_gb.mdout.3 & _MMPBSA_receptor_gb.mdout.3 12
>> frames processed
>> 13+13+12+12=50 and it's fine
>>
>> _MMPBSA_ligand_gb.mdout.0 1 frame processed then crashed
>> _MMPBSA_ligand_gb.mdout.1 1 frame processed then crashed
>> _MMPBSA_ligand_gb.mdout.2 0 frame processed then crashed
>> _MMPBSA_ligand_gb.mdout.3 1 frame processed then crashed
>>
>> For serial run:
>> I checked
>> _MMPBSA_complex_gb.mdout 50 frames processed
>> _MMPBSA_receptor_gb.mdout 62 frames processed
>> _MMPBSA_ligand_gb.mdout 100 frames processed
>>
>> Could anyone give me some explanation?
>>
>> Thanks
>> Ye
>>
>>
>> On Jul 6, 2011, at 9:51 AM, Ye Fan wrote:
>>
>>> Hi Bill,
>>>
>>> Yes, I've downloaded the bugfix.all at "
>> http://ambermd.org/bugfixesat.html" for version 1.5 and patched the source
>> codes before compiling them. If you could tell me which bug particularly you
>> are looking for, I can manually check it again.
>>>
>>> Thanks
>>> Ye
>>>
>>> On Jul 5, 2011, at 5:14 PM, Bill Miller III wrote:
>>>
>>>> Have you applied all the AmberTools 1.5 bugfixes? This was a bug that I
>>>> found in the code a while back, and I thought it had been added to the
>> known
>>>> patches.
>>>>
>>>> -Bill
>>>>
>>>> On Tue, Jul 5, 2011 at 3:53 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>>>>
>>>>> Hi Bill,
>>>>>
>>>>> This is the last part of _MMPBSA_receptor_pb.mdout file:
>>>>>
>>>>>
>>>>>
>> --------------------------------------------------------------------------------
>>>>> 4. RESULTS
>>>>>
>>>>>
>> --------------------------------------------------------------------------------
>>>>>
>>>>> POST-PROCESSING OF TRAJECTORY ENERGIES
>>>>> trajectory generated by ptraj
>>>>> minimizing coord set # 1
>>>>> Total surface charge 1.9723
>>>>> Reaction field energy -3570.1196
>>>>> Cavity solvation energy 54.6777
>>>>>
>>>>>
>>>>> Maximum number of minimization cycles reached.
>>>>>
>>>>>
>>>>> FINAL RESULTS
>>>>>
>>>>>
>>>>>
>>>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>>>> 1 -3.1384E+03 1.7292E+01 1.0289E+02 N 680
>>>>>
>>>>> BOND = 329.2644 ANGLE = 939.0290 DIHED =
>>>>> 1182.0229
>>>>> VDWAALS = -670.5602 EEL = -7995.5664 EPB =
>>>>> -3570.1813
>>>>> 1-4 VDW = 394.1857 1-4 EEL = 6198.7732 RESTRAINT =
>>>>> 0.0000
>>>>> ECAVITY = 54.6777 EDISPER = 0.0000
>>>>> minimization completed, ENE= -.31383551E+04 RMS= 0.172922E+02
>>>>> minimizing coord set # 2
>>>>> 67.611999999999995 5.7789999999999999 0.63300000000000001
>>>>> pb_fdfrc(): Atom out of focusing box 251 59
>> 44
>>>>>
>>>>>
>> ------------------------------------------------------------------------------------------------------------------------
>>>>>
>>>>> I hope it helps.
>>>>>
>>>>> Thanks
>>>>> Ye
>>>>>
>>>>> On Jul 5, 2011, at 11:57 AM, Bill Miller III wrote:
>>>>>
>>>>>> What is at the end of the _MMPBSA_receptor_pb.mdout file? There should
>> be
>>>>> an
>>>>>> error message or warning in that file that should help explain the
>> error
>>>>>> based on where the calculation ended.
>>>>>>
>>>>>> -Bill
>>>>>>
>>>>>> On Tue, Jul 5, 2011 at 12:50 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>>>>>>
>>>>>>> Hi Jason,
>>>>>>>
>>>>>>> I have added the "use_sander=1" in the $general section of input
>> file.
>>>>>>> However, the computation failed with sander error:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>> ================================================================================
>>>>>>> Reading command-line arguments and input files...
>>>>>>> Loading and checking parameter files for compatibility...
>>>>>>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
>>>>>>> sander found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/sander for GB
>>>>>>> calculations
>>>>>>> sander found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/sander for PB
>>>>>>> calculations
>>>>>>> Preparing trajectories for simulation...
>>>>>>> 50 frames were read in and processed by ptraj for use in calculation.
>>>>>>>
>>>>>>> Beginning GB calculations with sander...
>>>>>>> calculating complex contribution...
>>>>>>> calculating receptor contribution...
>>>>>>> calculating ligand contribution...
>>>>>>>
>>>>>>> Beginning PB calculations with sander...
>>>>>>> calculating complex contribution...
>>>>>>> calculating receptor contribution...
>>>>>>> Error: sander error during PB calculations!
>>>>>>> NOTE: All files have been retained for debugging purposes. Type
>>>>> MMPBSA.py
>>>>>>> --clean to erase these files.
>>>>>>>
>>>>>>>
>>>>>
>> ================================================================================
>>>>>>>
>>>>>>> I have serial sander built with gnu compiler.
>>>>>>>
>>>>>>> So, I went into the test folder of Amber11 and did `make
>> test.serial.MM
>>>>> `.
>>>>>>> It failed at (I wanted to test sander built):
>>>>>>> ========================================
>>>>>>> CALCULATING TEST: 02_MMPBSA_Stability
>>>>>>> ./Run.mmpbsa.test: Program error
>>>>>>> make: *** [test.mm_pbsa] Error 1
>>>>>>> ========================================
>>>>>>>
>>>>>>> I also did test under $AMBERHOME/AmberTools/test/mmpbsa_py.
>>>>>>>
>>>>>>> It failed at:
>>>>>>> ===========================
>>>>>>> cd 06_NAB_Nmode && ./Run.nmode
>>>>>>> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
>>>>>>> possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
>>>>>>> ...
>>>>>>> ...
>>>>>>> cd 08_Stability && ./Run.stability
>>>>>>> ./Run.stability: Program error
>>>>>>> make: *** [STABILITY] Error 1
>>>>>>> ===========================
>>>>>>>
>>>>>>> Any idea what's going wrong?
>>>>>>>
>>>>>>> Thank you very much
>>>>>>> Ye
>>>>>>>
>>>>>>>
>>>>>>> On Jul 2, 2011, at 7:18 PM, Jason Swails wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> If you have Amber11 available, try setting the variable
>> "use_sander=1"
>>>>> in
>>>>>>>> your MMPBSA input file (in the &general section). I'm not sure
>> what's
>>>>>>>> happening here, but your filesystem seems to be choking on
>> simultaneous
>>>>>>> file
>>>>>>>> accesses or something like that (perhaps the way NAB handles files
>> is
>>>>>>>> causing some grief, maybe you'll have better luck with sander,
>> although
>>>>>>> it
>>>>>>>> will take longer).
>>>>>>>>
>>>>>>>> HTH,
>>>>>>>> Jason
>>>>>>>>
>>>>>>>> On Fri, Jul 1, 2011 at 5:08 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>>>>>>>>
>>>>>>>>> Hi Jason,
>>>>>>>>>
>>>>>>>>> The serial version is only having some minor issues.
>>>>>>>>>
>>>>>>>>> Following is the output:
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>> Reading command-line arguments and input files...
>>>>>>>>> Loading and checking parameter files for compatibility...
>>>>>>>>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
>>>>>>>>> mmpbsa_py_energy found! Using
>>>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for GB
>>>>> calculations
>>>>>>>>> mmpbsa_py_energy found! Using
>>>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for PB
>>>>> calculations
>>>>>>>>> Preparing trajectories for simulation...
>>>>>>>>> 50 frames were read in and processed by ptraj for use in
>> calculation.
>>>>>>>>>
>>>>>>>>> Beginning GB calculations with mmpbsa_py_energy...
>>>>>>>>> calculating complex contribution...
>>>>>>>>> calculating receptor contribution...
>>>>>>>>> calculating ligand contribution...
>>>>>>>>>
>>>>>>>>> Beginning PB calculations with mmpbsa_py_energy...
>>>>>>>>> calculating complex contribution...
>>>>>>>>> PB Info in pb_read(): npopt has been overwritten with inp
>>>>>>>>> Total surface charge 2.9598
>>>>>>>>> Reaction field energy -4821.5307
>>>>>>>>> Cavity solvation energy 77.1504
>>>>>>>>> ...
>>>>>>>>> ...
>>>>>>>>> Reaction field energy -4763.0697
>>>>>>>>> Cavity solvation energy 78.8077
>>>>>>>>> calculating receptor contribution...
>>>>>>>>> PB Info in pb_read(): npopt has been overwritten with inp
>>>>>>>>> Total surface charge 1.9721
>>>>>>>>> Reaction field energy -3552.3284
>>>>>>>>> ...
>>>>>>>>> ...
>>>>>>>>> Reaction field energy -5066.6010
>>>>>>>>> Cavity solvation energy 62.5406
>>>>>>>>> calculating ligand contribution...
>>>>>>>>> PB Info in pb_read(): npopt has been overwritten with inp
>>>>>>>>> Total surface charge 0.9867
>>>>>>>>> Reaction field energy -2684.2835
>>>>>>>>> ...
>>>>>>>>> ...
>>>>>>>>> Reaction field energy -2737.6791
>>>>>>>>> Cavity solvation energy 34.1780
>>>>>>>>>
>>>>>>>>> Timing:
>>>>>>>>> Total setup time: 0.031 min.
>>>>>>>>> Creating trajectories with Ptraj: 0.084 min.
>>>>>>>>> Total calculation time: 29.421 min.
>>>>>>>>> Total GB calculation time (sander): 1.623 min.
>>>>>>>>> Total PB calculation time (sander): 27.798 min.
>>>>>>>>> Statistics calculation & output writing: 0.002 min.
>>>>>>>>> Total time taken: 29.538 min.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> MMPBSA.py Finished! Thank you for using. Please report any bugs to
>>>>>>>>> amber.ambermd.org
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>> Ye
>>>>>>>>>
>>>>>>>>> On Jul 1, 2011, at 11:39 AM, Jason Swails wrote:
>>>>>>>>>
>>>>>>>>>> Does it work in serial if you test it on just the first couple
>>>>> frames?
>>>>>>>>>>
>>>>>>>>>> On Fri, Jul 1, 2011 at 10:00 AM, Ye Fan <yefan.ncsa.uiuc.edu>
>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> I came across some errors when running MMPBSA.MPI. Following is
>> the
>>>>>>>>> output:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>> Running MMPBSA.MPI on 4 processors...
>>>>>>>>>>> Reading command-line arguments and input files...
>>>>>>>>>>> Loading and checking parameter files for compatibility...
>>>>>>>>>>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
>>>>>>>>>>> mmpbsa_py_energy found! Using
>>>>>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for GB
>>>>>>> calculations
>>>>>>>>>>> mmpbsa_py_energy found! Using
>>>>>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for PB
>>>>>>> calculations
>>>>>>>>>>> Preparing trajectories for simulation...
>>>>>>>>>>> 2150 frames were read in and processed by ptraj for use in
>>>>>>> calculation.
>>>>>>>>>>>
>>>>>>>>>>> Beginning GB calculations with mmpbsa_py_energy...
>>>>>>>>>>> calculating complex contribution...
>>>>>>>>>>> calculating receptor contribution...
>>>>>>>>>>> calculating ligand contribution...
>>>>>>>>>>> close failed in file object destructor:
>>>>>>>>>>> IOError: [Errno 9] Bad file descriptor
>>>>>>>>>>> close failed in file object destructor:
>>>>>>>>>>> IOError: [Errno 9] Bad file descriptor
>>>>>>>>>>> close failed in file object destructor:
>>>>>>>>>>> IOError: [Errno 9] Bad file descriptor
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>>>
>>>>>>>>>>> I have AmberTool 1.5 with Amber 11 fully patched and compiled
>> with
>>>>> gnu
>>>>>>>>>>> compiler. Mpi4py is built with openmpi-1.4.3.
>>>>>>>>>>>
>>>>>>>>>>> Any idea what's going wrong?
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>> Ye
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Bill Miller III
>>>>>> Quantum Theory Project,
>>>>>> University of Florida
>>>>>> Ph.D. Graduate Student
>>>>>> 352-392-6715
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Bill Miller III
>>>> Quantum Theory Project,
>>>> University of Florida
>>>> Ph.D. Graduate Student
>>>> 352-392-6715
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jul 15 2011 - 12:30:02 PDT
