Sat Oct 15 15:12:32 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+sph2.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 = amb2.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 Sat Oct 15 2011 at 15:12:32 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: SEP 227 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6160129 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): -30.88200 19.29800 ymin,ymax (A): -1.910000 48.37900 zmin,zma (A): -12.53100 45.26000 x,y,z range (A): 50.18000 50.28900 57.79100 scale (grids/A): 0.6160129 object centre (A): -5.792000 23.23450 16.36450 number of atom coordinates read : 2803 total number of charged atoms : 2653 net assigned charge : 4.039022 assigned positive charge : 426.8719 centred at (gu) : 90.26965 89.84827 92.34284 assigned negative charge : -422.8333 centred at (gu) : 90.55017 89.83200 92.28651 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6841 nv = 96 ne = 84 npr = 58285 no. pairs analyzed = 58285 no. exposed pairs = 3352 no. arc points = 23527 no. surface atoms = 1134 nbur = 1669 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 3712 m= 0 mr = 36 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2424 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1737469E-10 1.0871274E-08 midg,1,midg; midg,igrid,midg 1.8628477E-09 3.7640229E-09 1,midg,midg; igrid,midg,midg 1.9077955E-08 -1.6702693E-08 gauss-seidel spectral radius is 0.9863664 estimated iterations to convergence 70 setup time was (sec) 0.4300000 now iterating at: 15:12:33 rms-change max change #iterations 0.1331047 20.24880 at 10iterations 1.2379259E-02 1.805708 at 20iterations 1.2779760E-03 0.1713524 at 30iterations 2.2592366E-04 3.9804459E-02 at 40iterations 6.9805079E-05 1.2313843E-02 at 50iterations finished qdiffx linear iterations at : 15:12:36 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 6.9805079E-05 1.2313843E-02 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 15:12:36 3.743u 0.228s 0:04.38 90.4% 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 Sat Oct 15 2011 at 15:12:36 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: SEP 227 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.848039 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): -30.88200 19.29800 ymin,ymax (A): -1.910000 48.37900 zmin,zma (A): -12.53100 45.26000 x,y,z range (A): 50.18000 50.28900 57.79100 scale (grids/A): 1.848039 object centre (A): -5.792000 23.23450 16.36450 number of atom coordinates read : 2803 total number of charged atoms : 2653 net assigned charge : 4.039022 assigned positive charge : 426.8719 centred at (gu) : 90.80850 89.54450 97.02816 assigned negative charge : -422.8333 centred at (gu) : 91.65014 89.49571 96.85913 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 73462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23527 grid for indexing accessible points = 1.400000 m= 26642 mr = 50711 m= 4121 mr = 19401 m= 207 mr = 2483 m= 2 mr = 40 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 0.3900000 number of dielectric boundary points 31799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20763 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) : 0.6160129 object centre at (A) : -5.792000 23.23450 16.36450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5225826E-02 1.7835183E-02 midg,1,midg; midg,igrid,midg 9.3742047E-04 -1.4833765E-03 1,midg,midg; igrid,midg,midg 2.8408859E-02 -1.3544021E-02 gauss-seidel spectral radius is 0.9985689 estimated iterations to convergence 210 setup time was (sec) 0.6600000 now iterating at: 15:12:37 rms-change max change #iterations 4.238064 157.6962 at 10iterations 1.948372 69.20935 at 20iterations 0.8968579 29.51457 at 30iterations 0.4150069 13.30303 at 40iterations 0.1916564 6.451782 at 50iterations 8.8338122E-02 2.745615 at 60iterations 4.0688582E-02 1.250980 at 70iterations 1.8767018E-02 0.5682249 at 80iterations 8.6481050E-03 0.2688484 at 90iterations 3.9766668E-03 0.1240330 at 100iterations 1.8433437E-03 6.3282967E-02 at 110iterations 8.5260562E-04 2.6791573E-02 at 120iterations finished qdiffx linear iterations at : 15:12:45 total time elapsed so far: 8.720000 # loops : 120 mean,max change (kT/e) : 8.5260562E-04 2.6791573E-02 energy calculations done at 8.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.860000 DelPhi exited at 15:12:46 8.861u 0.271s 0:09.43 96.8% 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 Sat Oct 15 2011 at 15:12:46 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: SEP 227 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.772058 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): -30.88200 19.29800 ymin,ymax (A): -1.910000 48.37900 zmin,zma (A): -12.53100 45.26000 x,y,z range (A): 50.18000 50.28900 57.79100 scale (grids/A): 2.772058 object centre (A): -5.792000 23.23450 16.36450 number of atom coordinates read : 2803 total number of charged atoms : 2653 net assigned charge : 4.039022 assigned positive charge : 426.8719 centred at (gu) : 91.21266 89.31657 100.5418 assigned negative charge : -422.8333 centred at (gu) : 92.47518 89.24350 100.2888 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 169964 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23527 grid for indexing accessible points = 1.400000 m= 85683 mr = 123098 m= 31112 mr = 69690 m= 7132 mr = 24672 m= 926 mr = 5202 m= 32 mr = 540 m= 0 mr = 1 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 71646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 21220 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) : 1.848039 object centre at (A) : -5.792000 23.23450 16.36450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2878262 0.3644366 midg,1,midg; midg,igrid,midg -5.2081786E-02 -8.8494100E-02 1,midg,midg; igrid,midg,midg 0.1958138 -4.2109322E-02 gauss-seidel spectral radius is 0.9992436 estimated iterations to convergence 287 setup time was (sec) 1.260000 now iterating at: 15:12:47 rms-change max change #iterations 10.11220 354.2957 at 10iterations 5.914262 127.4548 at 20iterations 3.451030 88.07314 at 30iterations 1.998100 38.94055 at 40iterations 1.151467 24.28249 at 50iterations 0.6639983 13.64450 at 60iterations 0.3822244 7.692071 at 70iterations 0.2199258 4.407104 at 80iterations 0.1262895 2.241467 at 90iterations 7.2479144E-02 1.502843 at 100iterations 4.1563120E-02 0.7669983 at 110iterations 2.3831878E-02 0.4182739 at 120iterations 1.3695512E-02 0.2491302 at 130iterations 7.8406418E-03 0.1525879 at 140iterations 4.5041330E-03 8.2997561E-02 at 150iterations 2.5875340E-03 4.6099186E-02 at 160iterations 1.4909043E-03 3.0440807E-02 at 170iterations 8.6453592E-04 1.5705109E-02 at 180iterations finished qdiffx linear iterations at : 15:13:00 total time elapsed so far: 13.60000 # loops : 180 mean,max change (kT/e) : 8.6453592E-04 1.5705109E-02 energy calculations done at 13.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 15:13:00 13.737u 0.244s 0:14.28 97.8% 0+0k 0+0io 0pf+0w