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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Jul 15, 2011, at 2:27 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote: > 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 wit _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jul 15 2011 - 15:30:03 PDT