Mon Oct 10 00:04:30 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 00:04:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 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: 0.6226498 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): -7.719000 49.45600 ymin,ymax (A): -28.12300 23.11600 zmin,zma (A): -7.891000 40.55700 x,y,z range (A): 57.17500 51.23900 48.44800 scale (grids/A): 0.6226498 object centre (A): 20.86850 -2.503499 16.33300 number of atom coordinates read : 2570 total number of charged atoms : 2431 net assigned charge : 3.000007 assigned positive charge : 388.5539 centred at (gu) : 89.60933 91.14194 87.95761 assigned negative charge : -385.5547 centred at (gu) : 89.51608 91.21169 87.96126 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6447 nv = 96 ne = 84 npr = 52346 no. pairs analyzed = 52346 no. exposed pairs = 3072 no. arc points = 21560 no. surface atoms = 1047 nbur = 1523 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3541 m= 0 mr = 30 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3100000 number of dielectric boundary points 3177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2161 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8011 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5871955E-09 1.5900988E-09 midg,1,midg; midg,igrid,midg 5.9206897E-09 -3.0027287E-09 1,midg,midg; igrid,midg,midg -4.3587143E-09 8.4698524E-09 gauss-seidel spectral radius is 0.9866360 estimated iterations to convergence 71 setup time was (sec) 0.6500000 now iterating at: 00:04:31 rms-change max change #iterations 0.1273585 19.52813 at 10iterations 1.1657054E-02 1.909103 at 20iterations 1.0924266E-03 0.1541977 at 30iterations 1.0221494E-04 1.9428253E-02 at 40iterations 9.4551651E-06 1.4042854E-03 at 50iterations finished qdiffx linear iterations at : 00:04:35 total time elapsed so far: 5.120000 # loops : 50 mean,max change (kT/e) : 9.4551651E-06 1.4042854E-03 energy calculations done at 5.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.290000 DelPhi exited at 00:04:36 5.292u 0.469s 0:06.04 95.1% 0+0k 0+0io 6pf+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 00:04:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 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: 1.867949 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): -7.719000 49.45600 ymin,ymax (A): -28.12300 23.11600 zmin,zma (A): -7.891000 40.55700 x,y,z range (A): 57.17500 51.23900 48.44800 scale (grids/A): 1.867949 object centre (A): 20.86850 -2.503499 16.33300 number of atom coordinates read : 2570 total number of charged atoms : 2431 net assigned charge : 3.000007 assigned positive charge : 388.5539 centred at (gu) : 88.82763 93.42554 83.87259 assigned negative charge : -385.5547 centred at (gu) : 88.54797 93.63496 83.88383 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21560 grid for indexing accessible points = 1.400000 m= 23151 mr = 49072 m= 2847 mr = 16873 m= 115 mr = 1708 m= 0 mr = 42 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2167 time to turn everything in is 0.6100000 number of dielectric boundary points 29295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19048 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) : 0.6226498 object centre at (A) : 20.86850 -2.503499 16.33300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7377561E-02 6.6448608E-04 midg,1,midg; midg,igrid,midg 7.4259955E-03 5.4663857E-03 1,midg,midg; igrid,midg,midg -1.5604542E-02 3.5972513E-02 gauss-seidel spectral radius is 0.9985663 estimated iterations to convergence 209 setup time was (sec) 1.010000 now iterating at: 00:04:37 rms-change max change #iterations 4.013416 171.8799 at 10iterations 1.838006 62.33281 at 20iterations 0.8446676 27.54402 at 30iterations 0.3870447 13.57654 at 40iterations 0.1786268 5.577618 at 50iterations 8.1956141E-02 2.634229 at 60iterations 3.7600555E-02 1.183163 at 70iterations 1.7272942E-02 0.5204163 at 80iterations 7.9730814E-03 0.2729546 at 90iterations 3.6390682E-03 0.1238680 at 100iterations 1.6825282E-03 5.5922031E-02 at 110iterations 7.7088317E-04 2.3170471E-02 at 120iterations finished qdiffx linear iterations at : 00:04:49 total time elapsed so far: 12.37000 # loops : 120 mean,max change (kT/e) : 7.7088317E-04 2.3170471E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 00:04:49 12.554u 0.506s 0:13.35 97.7% 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 00:04:49 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 = 2570 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: 2.801924 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): -7.719000 49.45600 ymin,ymax (A): -28.12300 23.11600 zmin,zma (A): -7.891000 40.55700 x,y,z range (A): 57.17500 51.23900 48.44800 scale (grids/A): 2.801924 object centre (A): 20.86850 -2.503499 16.33300 number of atom coordinates read : 2570 total number of charged atoms : 2431 net assigned charge : 3.000007 assigned positive charge : 388.5539 centred at (gu) : 88.24126 95.13815 80.80874 assigned negative charge : -385.5547 centred at (gu) : 87.82195 95.45241 80.82581 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 164413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21560 grid for indexing accessible points = 1.400000 m= 77781 mr = 119281 m= 24621 mr = 63385 m= 4860 mr = 19558 m= 565 mr = 3561 m= 22 mr = 389 m= 0 mr = 8 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 7352 time to turn everything in is 1.500000 number of dielectric boundary points 66080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 19446 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) : 1.867949 object centre at (A) : 20.86850 -2.503499 16.33300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1693250 6.1519146E-03 midg,1,midg; midg,igrid,midg 3.1013420E-02 0.1594294 1,midg,midg; igrid,midg,midg -0.2036716 0.3253105 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 1.870000 now iterating at: 00:04:52 rms-change max change #iterations 9.413862 329.3013 at 10iterations 5.393304 112.9294 at 20iterations 3.074903 64.75896 at 30iterations 1.748270 34.63222 at 40iterations 0.9948535 21.03562 at 50iterations 0.5652725 11.10465 at 60iterations 0.3211246 6.176784 at 70iterations 0.1824546 3.493568 at 80iterations 0.1035505 1.991119 at 90iterations 5.8902092E-02 1.053028 at 100iterations 3.3519447E-02 0.6484680 at 110iterations 1.9082788E-02 0.3271427 at 120iterations 1.0845670E-02 0.2050018 at 130iterations 6.1700703E-03 0.1125259 at 140iterations 3.5080670E-03 6.3716888E-02 at 150iterations 1.9922582E-03 4.4961929E-02 at 160iterations 1.1362806E-03 2.1649361E-02 at 170iterations 6.4512150E-04 1.2005091E-02 at 180iterations finished qdiffx linear iterations at : 00:05:10 total time elapsed so far: 20.43000 # loops : 180 mean,max change (kT/e) : 6.4512150E-04 1.2005091E-02 energy calculations done at 20.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.59000 DelPhi exited at 00:05:11 20.592u 0.576s 0:21.43 98.7% 0+0k 0+0io 0pf+0w