Mon Oct 10 14:19:29 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 14:19:30 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5937985 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): -7.569000 44.06400 ymin,ymax (A): 13.27400 73.22700 zmin,zma (A): 54.62000 106.2010 x,y,z range (A): 51.63300 59.95300 51.58100 scale (grids/A): 0.5937985 object centre (A): 18.24750 43.25050 80.41051 number of atom coordinates read : 2594 total number of charged atoms : 2436 net assigned charge : -0.9999923 assigned positive charge : 382.2090 centred at (gu) : 90.09442 90.75676 89.57297 assigned negative charge : -383.2094 centred at (gu) : 89.90208 90.65746 89.60385 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6007 nv = 96 ne = 84 npr = 52591 no. pairs analyzed = 52591 no. exposed pairs = 3435 no. arc points = 23976 no. surface atoms = 1164 nbur = 1430 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 276 mr = 3025 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2409 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7554 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9461225E-10 -1.1756150E-09 midg,1,midg; midg,igrid,midg -2.8189970E-09 3.0321003E-09 1,midg,midg; igrid,midg,midg -6.0799330E-09 5.3211604E-09 gauss-seidel spectral radius is 0.9853266 estimated iterations to convergence 68 setup time was (sec) 0.6700000 now iterating at: 14:19:30 rms-change max change #iterations 9.8617621E-02 18.18023 at 10iterations 8.0817016E-03 1.320705 at 20iterations 6.8002235E-04 0.1221790 at 30iterations 5.5978286E-05 1.0245323E-02 at 40iterations 4.7924536E-06 8.5067749E-04 at 50iterations finished qdiffx linear iterations at : 14:19:34 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 4.7924536E-06 8.5067749E-04 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 14:19:34 4.238u 0.209s 0:04.78 92.6% 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 14:19:34 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.781396 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): -7.569000 44.06400 ymin,ymax (A): 13.27400 73.22700 zmin,zma (A): 54.62000 106.2010 x,y,z range (A): 51.63300 59.95300 51.58100 scale (grids/A): 1.781396 object centre (A): 18.24750 43.25050 80.41051 number of atom coordinates read : 2594 total number of charged atoms : 2436 net assigned charge : -0.9999923 assigned positive charge : 382.2090 centred at (gu) : 90.28262 92.26970 88.71855 assigned negative charge : -383.2094 centred at (gu) : 89.70600 91.97231 88.81128 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 65781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23976 grid for indexing accessible points = 1.400000 m= 20811 mr = 43961 m= 2431 mr = 14061 m= 116 mr = 1098 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 177 time to turn everything in is 0.6300000 number of dielectric boundary points 29994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18978 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) : 0.5937985 object centre at (A) : 18.24750 43.25050 80.41051 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4878469E-03 5.4733705E-06 midg,1,midg; midg,igrid,midg 7.7775243E-05 8.3236462E-03 1,midg,midg; igrid,midg,midg -2.7898479E-02 7.2936551E-03 gauss-seidel spectral radius is 0.9984424 estimated iterations to convergence 201 setup time was (sec) 0.9800000 now iterating at: 14:19:36 rms-change max change #iterations 3.666763 163.6050 at 10iterations 1.612822 57.38232 at 20iterations 0.7174692 26.77915 at 30iterations 0.3190985 11.21149 at 40iterations 0.1413661 5.181992 at 50iterations 6.2680528E-02 2.128774 at 60iterations 2.7888956E-02 0.9623642 at 70iterations 1.2413730E-02 0.4205276 at 80iterations 5.5241552E-03 0.1838951 at 90iterations 2.4550119E-03 8.8894844E-02 at 100iterations 1.0895353E-03 3.7189484E-02 at 110iterations 4.8566348E-04 2.0325661E-02 at 120iterations finished qdiffx linear iterations at : 14:19:44 total time elapsed so far: 9.220000 # loops : 120 mean,max change (kT/e) : 4.8566348E-04 2.0325661E-02 energy calculations done at 9.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 14:19:44 9.462u 0.291s 0:10.13 96.2% 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 14:19:45 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.672093 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): -7.569000 44.06400 ymin,ymax (A): 13.27400 73.22700 zmin,zma (A): 54.62000 106.2010 x,y,z range (A): 51.63300 59.95300 51.58100 scale (grids/A): 2.672093 object centre (A): 18.24750 43.25050 80.41051 number of atom coordinates read : 2594 total number of charged atoms : 2436 net assigned charge : -0.9999923 assigned positive charge : 382.2090 centred at (gu) : 90.42377 93.40443 88.07768 assigned negative charge : -383.2094 centred at (gu) : 89.55895 92.95834 88.21684 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 152749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23976 grid for indexing accessible points = 1.400000 m= 70471 mr = 107699 m= 21445 mr = 55281 m= 3900 mr = 15802 m= 403 mr = 2333 m= 17 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 583 time to turn everything in is 1.570000 number of dielectric boundary points 67689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 19484 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) : 1.781396 object centre at (A) : 18.24750 43.25050 80.41051 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2150065 2.2987161E-02 midg,1,midg; midg,igrid,midg -6.2346808E-03 2.3626355E-03 1,midg,midg; igrid,midg,midg -0.3827957 4.6225429E-02 gauss-seidel spectral radius is 0.9992106 estimated iterations to convergence 281 setup time was (sec) 1.960000 now iterating at: 14:19:47 rms-change max change #iterations 8.992552 287.9603 at 10iterations 5.202806 140.2379 at 20iterations 2.968345 71.05527 at 30iterations 1.696070 42.42049 at 40iterations 0.9669322 20.31691 at 50iterations 0.5488061 12.81662 at 60iterations 0.3109462 7.525018 at 70iterations 0.1753029 3.582150 at 80iterations 9.9399842E-02 2.101315 at 90iterations 5.6293927E-02 1.271584 at 100iterations 3.1772844E-02 0.6467705 at 110iterations 1.7935835E-02 0.3757858 at 120iterations 1.0134090E-02 0.2258749 at 130iterations 5.7131913E-03 0.1278124 at 140iterations 3.2253149E-03 6.6749573E-02 at 150iterations 1.8143582E-03 3.6133528E-02 at 160iterations 1.0230500E-03 2.1130562E-02 at 170iterations 5.7850737E-04 1.1452675E-02 at 180iterations finished qdiffx linear iterations at : 14:20:00 total time elapsed so far: 15.32000 # loops : 180 mean,max change (kT/e) : 5.7850737E-04 1.1452675E-02 energy calculations done at 15.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.56000 DelPhi exited at 14:20:01 15.564u 0.291s 0:16.28 97.3% 0+0k 0+0io 0pf+0w