Sat Oct 15 15:21:51 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 15:21:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3348 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: 0.5424845 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): 113.3730 170.7110 ymin,ymax (A): 18.16000 66.12000 zmin,zma (A): -11.11100 54.51300 x,y,z range (A): 57.33800 47.96000 65.62400 scale (grids/A): 0.5424845 object centre (A): 142.0420 42.14000 21.70100 number of atom coordinates read : 3348 total number of charged atoms : 3196 net assigned charge : 1.500025 assigned positive charge : 510.3126 centred at (gu) : 90.23466 89.98890 88.45174 assigned negative charge : -508.8137 centred at (gu) : 90.38982 90.11798 88.32229 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6235 nv = 96 ne = 84 npr = 67726 no. pairs analyzed = 67726 no. exposed pairs = 4046 no. arc points = 28934 no. surface atoms = 1364 nbur = 1984 mkacc time = 0.1700000 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 = 1.568000 m= 227 mr = 3248 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2957 ## 425 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8266 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1525707E-09 6.4357514E-10 midg,1,midg; midg,igrid,midg 9.4766706E-10 -7.6918594E-10 1,midg,midg; igrid,midg,midg 1.0484431E-09 -1.0097500E-09 gauss-seidel spectral radius is 0.9825082 estimated iterations to convergence 62 setup time was (sec) 0.7100000 now iterating at: 15:21:52 rms-change max change #iterations 7.4831419E-02 14.22458 at 10iterations 4.9373582E-03 0.8271236 at 20iterations 3.4219865E-04 5.4748535E-02 at 30iterations 3.5673125E-05 7.0343018E-03 at 40iterations 7.7982850E-06 1.4839172E-03 at 50iterations finished qdiffx linear iterations at : 15:21:58 total time elapsed so far: 5.330000 # loops : 50 mean,max change (kT/e) : 7.7982850E-06 1.4839172E-03 energy calculations done at 5.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.490000 DelPhi exited at 15:21:59 5.490u 0.448s 0:08.01 74.0% 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 15:21:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3348 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.627453 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): 113.3730 170.7110 ymin,ymax (A): 18.16000 66.12000 zmin,zma (A): -11.11100 54.51300 x,y,z range (A): 57.33800 47.96000 65.62400 scale (grids/A): 1.627453 object centre (A): 142.0420 42.14000 21.70100 number of atom coordinates read : 3348 total number of charged atoms : 3196 net assigned charge : 1.500025 assigned positive charge : 510.3126 centred at (gu) : 90.70339 89.96588 85.35437 assigned negative charge : -508.8137 centred at (gu) : 91.16894 90.35330 84.96649 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68166 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28934 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21846 mr = 45877 m= 2271 mr = 15349 m= 64 mr = 1076 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1736 time to turn everything in is 0.6000000 number of dielectric boundary points 30045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 402 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 24457 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) : 0.5424845 object centre at (A) : 142.0420 42.14000 21.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0761468E-02 8.6187832E-03 midg,1,midg; midg,igrid,midg 4.2935503E-03 -3.7676659E-03 1,midg,midg; igrid,midg,midg 2.2522738E-02 3.1382733E-04 gauss-seidel spectral radius is 0.9982069 estimated iterations to convergence 188 setup time was (sec) 0.9500000 now iterating at: 15:22:00 rms-change max change #iterations 3.534876 165.1580 at 10iterations 1.476138 60.19541 at 20iterations 0.6191010 20.86135 at 30iterations 0.2602659 9.699066 at 40iterations 0.1090490 3.988268 at 50iterations 4.5668010E-02 1.597548 at 60iterations 1.9190090E-02 0.6857815 at 70iterations 8.0294050E-03 0.3106384 at 80iterations 3.3768679E-03 0.1173706 at 90iterations 1.4163472E-03 5.0621033E-02 at 100iterations 5.9858343E-04 2.0031929E-02 at 110iterations 2.5316767E-04 9.4032288E-03 at 120iterations finished qdiffx linear iterations at : 15:22:22 total time elapsed so far: 12.29000 # loops : 120 mean,max change (kT/e) : 2.5316767E-04 9.4032288E-03 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 15:22:25 12.464u 0.523s 0:26.46 49.0% 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 15:22:25 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 = 3348 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.441180 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): 113.3730 170.7110 ymin,ymax (A): 18.16000 66.12000 zmin,zma (A): -11.11100 54.51300 x,y,z range (A): 57.33800 47.96000 65.62400 scale (grids/A): 2.441180 object centre (A): 142.0420 42.14000 21.70100 number of atom coordinates read : 3348 total number of charged atoms : 3196 net assigned charge : 1.500025 assigned positive charge : 510.3126 centred at (gu) : 91.05461 89.94855 83.03145 assigned negative charge : -508.8137 centred at (gu) : 91.75319 90.52991 82.44954 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 158485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28934 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 74731 mr = 112766 m= 22064 mr = 59414 m= 3526 mr = 16810 m= 222 mr = 2232 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 5870 time to turn everything in is 1.450000 number of dielectric boundary points 67723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 25530 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) : 1.627453 object centre at (A) : 142.0420 42.14000 21.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4538049E-02 0.1084174 midg,1,midg; midg,igrid,midg 5.2336723E-02 -1.8459219E-02 1,midg,midg; igrid,midg,midg 0.2969654 5.5745244E-02 gauss-seidel spectral radius is 0.9991516 estimated iterations to convergence 271 setup time was (sec) 1.830000 now iterating at: 15:22:28 rms-change max change #iterations 9.064279 277.0791 at 10iterations 5.084893 124.7993 at 20iterations 2.841577 82.12151 at 30iterations 1.583632 33.63585 at 40iterations 0.8776012 19.30751 at 50iterations 0.4871712 9.577789 at 60iterations 0.2700654 5.132931 at 70iterations 0.1491752 3.048622 at 80iterations 8.2531884E-02 1.776626 at 90iterations 4.5483548E-02 0.9043999 at 100iterations 2.5091104E-02 0.5233765 at 110iterations 1.3890478E-02 0.2632141 at 120iterations 7.6805563E-03 0.1474895 at 130iterations 4.2409059E-03 8.4041595E-02 at 140iterations 2.3414625E-03 4.9373627E-02 at 150iterations 1.2942920E-03 2.7151585E-02 at 160iterations 7.1695057E-04 1.4560699E-02 at 170iterations 3.9837946E-04 8.0232620E-03 at 180iterations finished qdiffx linear iterations at : 15:22:54 total time elapsed so far: 21.79000 # loops : 180 mean,max change (kT/e) : 3.9837946E-04 8.0232620E-03 energy calculations done at 21.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.97000 DelPhi exited at 15:22:55 21.973u 0.602s 0:29.31 77.0% 0+0k 0+0io 0pf+0w