Sat Oct 15 13:14:39 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 Sat Oct 15 2011 at 13:14:39 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 = 3219 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: 0.5110170 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): -35.78200 12.72100 ymin,ymax (A): 31.21100 85.33700 zmin,zma (A): -16.74900 52.91600 x,y,z range (A): 48.50300 54.12600 69.66500 scale (grids/A): 0.5110170 object centre (A): -11.53050 58.27400 18.08350 number of atom coordinates read : 3219 total number of charged atoms : 3077 net assigned charge : 3.500008 assigned positive charge : 498.2716 centred at (gu) : 90.03608 88.88708 90.30581 assigned negative charge : -494.7727 centred at (gu) : 90.10181 88.78309 90.17773 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5400 nv = 96 ne = 84 npr = 62577 no. pairs analyzed = 62577 no. exposed pairs = 4371 no. arc points = 30352 no. surface atoms = 1469 nbur = 1750 mkacc time = 0.2000000 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 = 1.652000 m= 176 mr = 2536 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2999 ## 454 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 7180 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7088612E-10 3.0650008E-10 midg,1,midg; midg,igrid,midg -1.9017221E-10 1.7900764E-10 1,midg,midg; igrid,midg,midg 1.6994162E-10 -6.9392936E-11 gauss-seidel spectral radius is 0.9803118 estimated iterations to convergence 59 setup time was (sec) 0.8300000 now iterating at: 13:14:40 rms-change max change #iterations 5.3914759E-02 9.924228 at 10iterations 3.0191271E-03 0.5447369 at 20iterations 2.0269869E-04 3.2461166E-02 at 30iterations 2.2929264E-05 2.9344559E-03 at 40iterations 3.7338648E-06 3.7860870E-04 at 50iterations finished qdiffx linear iterations at : 13:14:44 total time elapsed so far: 4.860000 # loops : 50 mean,max change (kT/e) : 3.7338648E-06 3.7860870E-04 energy calculations done at 4.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.100000 DelPhi exited at 13:14:45 5.102u 0.433s 0:05.98 92.4% 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 13:14:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3219 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: 1.533051 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): -35.78200 12.72100 ymin,ymax (A): 31.21100 85.33700 zmin,zma (A): -16.74900 52.91600 x,y,z range (A): 48.50300 54.12600 69.66500 scale (grids/A): 1.533051 object centre (A): -11.53050 58.27400 18.08350 number of atom coordinates read : 3219 total number of charged atoms : 3077 net assigned charge : 3.500008 assigned positive charge : 498.2716 centred at (gu) : 90.10754 86.66060 90.91668 assigned negative charge : -494.7727 centred at (gu) : 90.30486 86.34863 90.53296 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 60921 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30352 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15575 mr = 39336 m= 1145 mr = 9758 m= 24 mr = 410 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 0.6300000 number of dielectric boundary points 28161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 419 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23094 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) : 0.5110170 object centre at (A) : -11.53050 58.27400 18.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0828874E-02 1.1547449E-02 midg,1,midg; midg,igrid,midg -3.0893809E-03 2.7933487E-04 1,midg,midg; igrid,midg,midg 3.0305935E-03 2.5670847E-03 gauss-seidel spectral radius is 0.9979600 estimated iterations to convergence 176 setup time was (sec) 0.9800000 now iterating at: 13:14:47 rms-change max change #iterations 3.035638 164.3875 at 10iterations 1.198740 52.27480 at 20iterations 0.4735596 17.53424 at 30iterations 0.1863761 7.148947 at 40iterations 7.4016087E-02 3.515970 at 50iterations 2.9240698E-02 1.159495 at 60iterations 1.1576952E-02 0.4946890 at 70iterations 4.5737657E-03 0.1841545 at 80iterations 1.8132791E-03 7.9368591E-02 at 90iterations 7.2028302E-04 2.7898788E-02 at 100iterations 2.8624551E-04 1.1411667E-02 at 110iterations 1.1342169E-04 4.1828156E-03 at 120iterations finished qdiffx linear iterations at : 13:15:01 total time elapsed so far: 11.02000 # loops : 120 mean,max change (kT/e) : 1.1342169E-04 4.1828156E-03 energy calculations done at 11.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 13:15:02 11.250u 0.527s 0:17.17 68.5% 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 13:15:02 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 = 3219 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: 2.299577 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): -35.78200 12.72100 ymin,ymax (A): 31.21100 85.33700 zmin,zma (A): -16.74900 52.91600 x,y,z range (A): 48.50300 54.12600 69.66500 scale (grids/A): 2.299577 object centre (A): -11.53050 58.27400 18.08350 number of atom coordinates read : 3219 total number of charged atoms : 3077 net assigned charge : 3.500008 assigned positive charge : 498.2716 centred at (gu) : 90.16120 84.99068 91.37473 assigned negative charge : -494.7727 centred at (gu) : 90.45724 84.52285 90.79931 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 142172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30352 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 58083 mr = 97739 m= 12534 mr = 43770 m= 1558 mr = 8554 m= 84 mr = 855 m= 0 mr = 20 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 1024 time to turn everything in is 1.500000 number of dielectric boundary points 63493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 24536 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) : 1.533051 object centre at (A) : -11.53050 58.27400 18.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1289819 0.1524472 midg,1,midg; midg,igrid,midg -1.6392235E-02 -1.0101179E-02 1,midg,midg; igrid,midg,midg 4.0269177E-02 4.7359101E-02 gauss-seidel spectral radius is 0.9990830 estimated iterations to convergence 261 setup time was (sec) 1.870000 now iterating at: 13:15:05 rms-change max change #iterations 8.407234 316.1249 at 10iterations 4.696674 134.7406 at 20iterations 2.585028 67.48818 at 30iterations 1.423380 36.04405 at 40iterations 0.7772920 18.87037 at 50iterations 0.4235686 9.742527 at 60iterations 0.2305092 5.757917 at 70iterations 0.1248579 2.974987 at 80iterations 6.7580648E-02 1.730049 at 90iterations 3.6659785E-02 0.7712250 at 100iterations 1.9776316E-02 0.4399300 at 110iterations 1.0709000E-02 0.2235117 at 120iterations 5.7539246E-03 0.1285477 at 130iterations 3.1089874E-03 6.4899445E-02 at 140iterations 1.6754788E-03 3.6167145E-02 at 150iterations 9.0427062E-04 2.0835161E-02 at 160iterations 4.8793398E-04 1.0579586E-02 at 170iterations 2.6282866E-04 6.4315796E-03 at 180iterations finished qdiffx linear iterations at : 13:15:25 total time elapsed so far: 18.54000 # loops : 180 mean,max change (kT/e) : 2.6282866E-04 6.4315796E-03 energy calculations done at 18.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.75000 DelPhi exited at 13:15:26 18.759u 0.549s 0:23.91 80.6% 0+0k 0+0io 0pf+0w