Mon Oct 10 17:11:32 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:11:32 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2926 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6228895 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 13.75100 70.90400 ymin,ymax (A): 3.818000 50.93500 zmin,zma (A): 6.951000 63.30300 x,y,z range (A): 57.15300 47.11700 56.35200 scale (grids/A): 0.6228895 object centre (A): 42.32750 27.37650 35.12700 number of atom coordinates read : 2926 total number of charged atoms : 2784 net assigned charge : -4.499969 assigned positive charge : 438.1029 centred at (gu) : 89.15247 90.40770 91.11715 assigned negative charge : -442.6041 centred at (gu) : 89.04598 90.53488 91.23158 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7715 nv = 96 ne = 84 npr = 57950 no. pairs analyzed = 57950 no. exposed pairs = 3844 no. arc points = 27399 no. surface atoms = 1301 nbur = 1625 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 4049 m= 3 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2702 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9400 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3342974E-09 -1.6920495E-08 midg,1,midg; midg,igrid,midg 6.0330296E-09 -1.5631683E-08 1,midg,midg; igrid,midg,midg -1.5123923E-08 4.0832475E-09 gauss-seidel spectral radius is 0.9866906 estimated iterations to convergence 71 setup time was (sec) 0.5200000 now iterating at: 17:11:32 rms-change max change #iterations 0.1360874 19.56175 at 10iterations 1.2550268E-02 1.810001 at 20iterations 1.1585315E-03 0.1836433 at 30iterations 1.1040054E-04 1.5830994E-02 at 40iterations 1.0621979E-05 1.5449524E-03 at 50iterations finished qdiffx linear iterations at : 17:11:35 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.0621979E-05 1.5449524E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 17:11:35 3.089u 0.141s 0:03.53 91.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:11:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2926 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.868668 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 13.75100 70.90400 ymin,ymax (A): 3.818000 50.93500 zmin,zma (A): 6.951000 63.30300 x,y,z range (A): 57.15300 47.11700 56.35200 scale (grids/A): 1.868668 object centre (A): 42.32750 27.37650 35.12700 number of atom coordinates read : 2926 total number of charged atoms : 2784 net assigned charge : -4.499969 assigned positive charge : 438.1029 centred at (gu) : 87.45679 91.22211 93.35054 assigned negative charge : -442.6041 centred at (gu) : 87.13744 91.60420 93.69446 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27399 grid for indexing accessible points = 1.400000 m= 28340 mr = 56382 m= 3937 mr = 20122 m= 199 mr = 2249 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1264 time to turn everything in is 0.5600000 number of dielectric boundary points 37250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 21868 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6228895 object centre at (A) : 42.32750 27.37650 35.12700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6305779E-03 -1.8411595E-02 midg,1,midg; midg,igrid,midg 2.1350462E-04 -2.8704319E-02 1,midg,midg; igrid,midg,midg -5.6098398E-02 2.1564225E-02 gauss-seidel spectral radius is 0.9986280 estimated iterations to convergence 214 setup time was (sec) 0.8300000 now iterating at: 17:11:36 rms-change max change #iterations 4.390008 194.4351 at 10iterations 2.043554 68.15816 at 20iterations 0.9493551 29.89266 at 30iterations 0.4434139 17.03956 at 40iterations 0.2070347 6.487015 at 50iterations 9.6616931E-02 2.796747 at 60iterations 4.5123126E-02 1.291705 at 70iterations 2.1079725E-02 0.6745014 at 80iterations 9.8403441E-03 0.2711538 at 90iterations 4.5980578E-03 0.1536407 at 100iterations 2.1444592E-03 6.7265511E-02 at 110iterations 1.0024651E-03 3.2043457E-02 at 120iterations finished qdiffx linear iterations at : 17:11:42 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 1.0024651E-03 3.2043457E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 17:11:43 6.918u 0.148s 0:07.44 94.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:11:43 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2926 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.803002 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 13.75100 70.90400 ymin,ymax (A): 3.818000 50.93500 zmin,zma (A): 6.951000 63.30300 x,y,z range (A): 57.15300 47.11700 56.35200 scale (grids/A): 2.803002 object centre (A): 42.32750 27.37650 35.12700 number of atom coordinates read : 2926 total number of charged atoms : 2784 net assigned charge : -4.499969 assigned positive charge : 438.1029 centred at (gu) : 86.18491 91.83295 95.02559 assigned negative charge : -442.6041 centred at (gu) : 85.70612 92.40622 95.54166 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 193197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27399 grid for indexing accessible points = 1.400000 m= 93221 mr = 137105 m= 31546 mr = 74517 m= 6623 mr = 24559 m= 759 mr = 4684 m= 47 mr = 458 m= 0 mr = 9 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 4107 time to turn everything in is 1.370000 number of dielectric boundary points 84061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 22270 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.868668 object centre at (A) : 42.32750 27.37650 35.12700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2911498 7.4125499E-02 midg,1,midg; midg,igrid,midg -2.8949803E-02 -0.2465401 1,midg,midg; igrid,midg,midg -0.6955117 0.3089404 gauss-seidel spectral radius is 0.9992795 estimated iterations to convergence 294 setup time was (sec) 1.650000 now iterating at: 17:11:45 rms-change max change #iterations 10.54410 352.5688 at 10iterations 6.275535 138.8106 at 20iterations 3.693418 80.78352 at 30iterations 2.170761 45.22222 at 40iterations 1.267725 25.81538 at 50iterations 0.7385389 15.84088 at 60iterations 0.4307588 8.078028 at 70iterations 0.2499366 4.972260 at 80iterations 0.1453597 2.532930 at 90iterations 8.4368169E-02 1.656441 at 100iterations 4.8977368E-02 0.8591843 at 110iterations 2.8352557E-02 0.6110096 at 120iterations 1.6429592E-02 0.3040771 at 130iterations 9.5344288E-03 0.1931868 at 140iterations 5.5209692E-03 9.2746735E-02 at 150iterations 3.1969352E-03 5.2941084E-02 at 160iterations 1.8554883E-03 3.5213470E-02 at 170iterations 1.0783437E-03 1.8844604E-02 at 180iterations finished qdiffx linear iterations at : 17:11:54 total time elapsed so far: 11.09000 # loops : 180 mean,max change (kT/e) : 1.0783437E-03 1.8844604E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.26000 DelPhi exited at 17:11:55 11.263u 0.167s 0:11.73 97.3% 0+0k 0+0io 0pf+0w