Mon Oct 10 12:11:47 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 Mon Oct 10 2011 at 12:11:47 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7427034 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): 9.698000 56.25100 ymin,ymax (A): -9.043000 36.10600 zmin,zma (A): -3.383000 44.55000 x,y,z range (A): 46.55300 45.14900 47.93300 scale (grids/A): 0.7427034 object centre (A): 32.97450 13.53150 20.58350 number of atom coordinates read : 2117 total number of charged atoms : 1976 net assigned charge : -6.846981 assigned positive charge : 318.1199 centred at (gu) : 88.92321 90.68862 89.92598 assigned negative charge : -324.9670 centred at (gu) : 88.91846 90.76852 90.12101 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8107 nv = 96 ne = 84 npr = 43483 no. pairs analyzed = 43483 no. exposed pairs = 2740 no. arc points = 19223 no. surface atoms = 925 nbur = 1192 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 590 mr = 4509 m= 5 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2500000 number of dielectric boundary points 4064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1546 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8393 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2663526E-08 -3.3849463E-07 midg,1,midg; midg,igrid,midg -3.6570427E-08 -2.4374347E-07 1,midg,midg; igrid,midg,midg -1.6055344E-07 -1.0056942E-07 gauss-seidel spectral radius is 0.9905543 estimated iterations to convergence 84 setup time was (sec) 0.4800000 now iterating at: 12:11:47 rms-change max change #iterations 0.2543290 35.10421 at 10iterations 3.3900257E-02 4.763798 at 20iterations 4.6472857E-03 0.5817032 at 30iterations 6.2736165E-04 8.0688953E-02 at 40iterations 8.5217369E-05 1.0741234E-02 at 50iterations finished qdiffx linear iterations at : 12:11:50 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 8.5217369E-05 1.0741234E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 12:11:51 3.288u 0.216s 0:04.04 86.3% 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 12:11:51 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.228110 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): 9.698000 56.25100 ymin,ymax (A): -9.043000 36.10600 zmin,zma (A): -3.383000 44.55000 x,y,z range (A): 46.55300 45.14900 47.93300 scale (grids/A): 2.228110 object centre (A): 32.97450 13.53150 20.58350 number of atom coordinates read : 2117 total number of charged atoms : 1976 net assigned charge : -6.846981 assigned positive charge : 318.1199 centred at (gu) : 86.76981 92.06593 89.77774 assigned negative charge : -324.9670 centred at (gu) : 86.75535 92.30554 90.36307 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19223 grid for indexing accessible points = 1.400000 m= 34684 mr = 58179 m= 7562 mr = 26608 m= 750 mr = 5286 m= 26 mr = 437 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 743 time to turn everything in is 0.6300000 number of dielectric boundary points 36933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15740 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) : 0.7427034 object centre at (A) : 32.97450 13.53150 20.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9386953E-03 -0.1205408 midg,1,midg; midg,igrid,midg -3.2047685E-02 -4.4603430E-02 1,midg,midg; igrid,midg,midg -2.5543785E-02 5.1005534E-04 gauss-seidel spectral radius is 0.9989328 estimated iterations to convergence 242 setup time was (sec) 0.9200000 now iterating at: 12:11:52 rms-change max change #iterations 5.145401 203.8065 at 10iterations 2.611912 82.21877 at 20iterations 1.334865 38.94420 at 30iterations 0.6835588 20.64164 at 40iterations 0.3476789 12.51052 at 50iterations 0.1783500 4.782898 at 60iterations 9.0999804E-02 2.573837 at 70iterations 4.6571206E-02 1.242664 at 80iterations 2.3733195E-02 0.6599975 at 90iterations 1.2159439E-02 0.3412342 at 100iterations 6.2103863E-03 0.1804886 at 110iterations 3.1762267E-03 9.8519802E-02 at 120iterations finished qdiffx linear iterations at : 12:11:58 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 3.1762267E-03 9.8519802E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 12:11:59 7.610u 0.217s 0:08.16 95.8% 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 Mon Oct 10 2011 at 12:11:59 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.342165 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): 9.698000 56.25100 ymin,ymax (A): -9.043000 36.10600 zmin,zma (A): -3.383000 44.55000 x,y,z range (A): 46.55300 45.14900 47.93300 scale (grids/A): 3.342165 object centre (A): 32.97450 13.53150 20.58350 number of atom coordinates read : 2117 total number of charged atoms : 1976 net assigned charge : -6.846981 assigned positive charge : 318.1199 centred at (gu) : 85.15466 93.09896 89.66665 assigned negative charge : -324.9670 centred at (gu) : 85.13300 93.45827 90.54457 start vw surface at 0.1400000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 193960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19223 grid for indexing accessible points = 1.400000 m= 105136 mr = 139651 m= 46444 mr = 87622 m= 14693 mr = 38922 m= 3134 mr = 11708 m= 439 mr = 2357 m= 19 mr = 278 m= 0 mr = 4 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2335 time to turn everything in is 1.980000 number of dielectric boundary points 83283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 15808 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) : 2.228110 object centre at (A) : 32.97450 13.53150 20.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1255630 -1.113085 midg,1,midg; midg,igrid,midg -0.2709575 -0.1920577 1,midg,midg; igrid,midg,midg -0.3018022 -3.4283455E-02 gauss-seidel spectral radius is 0.9993212 estimated iterations to convergence 303 setup time was (sec) 2.300000 now iterating at: 12:12:02 rms-change max change #iterations 11.10533 286.5238 at 10iterations 6.561555 129.5066 at 20iterations 3.871869 75.63325 at 30iterations 2.281631 42.49779 at 40iterations 1.344842 22.00034 at 50iterations 0.7933106 14.24881 at 60iterations 0.4665526 8.255224 at 70iterations 0.2745656 4.444262 at 80iterations 0.1614071 2.518812 at 90iterations 9.5009588E-02 1.636051 at 100iterations 5.5912998E-02 0.9069595 at 110iterations 3.2829307E-02 0.5415421 at 120iterations 1.9304363E-02 0.3151040 at 130iterations 1.1343717E-02 0.1871195 at 140iterations 6.6831210E-03 0.1097181 at 150iterations 3.9247097E-03 6.6703796E-02 at 160iterations 2.3120230E-03 3.5855293E-02 at 170iterations 1.3580008E-03 2.2975922E-02 at 180iterations finished qdiffx linear iterations at : 12:12:12 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 1.3580008E-03 2.2975922E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 12:12:13 13.087u 0.264s 0:14.08 94.7% 0+0k 0+0io 0pf+0w