Tue Oct 11 03:15:04 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 Tue Oct 11 2011 at 03:15:04 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 = 3432 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: 0.5386919 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): 4.450000 70.53600 ymin,ymax (A): 32.08700 94.04300 zmin,zma (A): 25.06000 79.39500 x,y,z range (A): 66.08601 61.95600 54.33501 scale (grids/A): 0.5386919 object centre (A): 37.49300 63.06500 52.22750 number of atom coordinates read : 3432 total number of charged atoms : 3291 net assigned charge : -6.499979 assigned positive charge : 516.2742 centred at (gu) : 87.75932 91.67952 88.30560 assigned negative charge : -522.7758 centred at (gu) : 87.70227 91.67109 88.33944 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6426 nv = 96 ne = 84 npr = 69496 no. pairs analyzed = 69496 no. exposed pairs = 4434 no. arc points = 30723 no. surface atoms = 1491 nbur = 1941 mkacc time = 0.1200000 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 = 1.596000 m= 249 mr = 3284 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3194 ## 466 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8497 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4278485E-10 -3.2592745E-10 midg,1,midg; midg,igrid,midg -2.2938119E-10 -3.6988596E-10 1,midg,midg; igrid,midg,midg -1.1117767E-09 1.5980668E-11 gauss-seidel spectral radius is 0.9822713 estimated iterations to convergence 62 setup time was (sec) 0.4100000 now iterating at: 03:15:05 rms-change max change #iterations 7.2908998E-02 11.23559 at 10iterations 4.9883071E-03 0.7077103 at 20iterations 4.6515735E-04 6.3946247E-02 at 30iterations 8.9185225E-05 1.2402892E-02 at 40iterations 2.2073682E-05 3.1978935E-03 at 50iterations finished qdiffx linear iterations at : 03:15:08 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.2073682E-05 3.1978935E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 03:15:08 3.389u 0.175s 0:04.03 88.0% 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 Tue Oct 11 2011 at 03:15:08 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 = 3432 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: 1.616076 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): 4.450000 70.53600 ymin,ymax (A): 32.08700 94.04300 zmin,zma (A): 25.06000 79.39500 x,y,z range (A): 66.08601 61.95600 54.33501 scale (grids/A): 1.616076 object centre (A): 37.49300 63.06500 52.22750 number of atom coordinates read : 3432 total number of charged atoms : 3291 net assigned charge : -6.499979 assigned positive charge : 516.2742 centred at (gu) : 83.27727 95.03747 84.91621 assigned negative charge : -522.7758 centred at (gu) : 83.10649 95.01294 85.01789 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30723 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21623 mr = 47078 m= 2208 mr = 14727 m= 60 mr = 1092 m= 0 mr = 5 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 583 time to turn everything in is 0.3600000 number of dielectric boundary points 31547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 424 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 25138 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) : 0.5386919 object centre at (A) : 37.49300 63.06500 52.22750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2630696E-03 -2.6192507E-03 midg,1,midg; midg,igrid,midg -3.2533808E-03 4.8306980E-03 1,midg,midg; igrid,midg,midg -2.0294864E-02 2.8427944E-02 gauss-seidel spectral radius is 0.9981847 estimated iterations to convergence 186 setup time was (sec) 0.5800000 now iterating at: 03:15:09 rms-change max change #iterations 3.496604 175.3747 at 10iterations 1.451555 69.26234 at 20iterations 0.6049182 23.79134 at 30iterations 0.2518506 11.62924 at 40iterations 0.1049859 3.919540 at 50iterations 4.3823980E-02 1.456187 at 60iterations 1.8311318E-02 0.6107035 at 70iterations 7.6607997E-03 0.2738695 at 80iterations 3.2407783E-03 0.1153641 at 90iterations 1.3759041E-03 4.8492432E-02 at 100iterations 6.0006499E-04 2.1323204E-02 at 110iterations 2.7236110E-04 1.0651588E-02 at 120iterations finished qdiffx linear iterations at : 03:15:16 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.7236110E-04 1.0651588E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 03:15:17 7.791u 0.189s 0:08.26 96.4% 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 Tue Oct 11 2011 at 03:15:17 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 = 3432 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: 2.424114 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): 4.450000 70.53600 ymin,ymax (A): 32.08700 94.04300 zmin,zma (A): 25.06000 79.39500 x,y,z range (A): 66.08601 61.95600 54.33501 scale (grids/A): 2.424114 object centre (A): 37.49300 63.06500 52.22750 number of atom coordinates read : 3432 total number of charged atoms : 3291 net assigned charge : -6.499979 assigned positive charge : 516.2742 centred at (gu) : 79.91544 97.55600 82.37406 assigned negative charge : -522.7758 centred at (gu) : 79.65956 97.51931 82.52665 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30723 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 75570 mr = 115606 m= 21129 mr = 59138 m= 3427 mr = 15780 m= 195 mr = 2283 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2153 time to turn everything in is 0.8700000 number of dielectric boundary points 71199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 26291 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) : 1.616076 object centre at (A) : 37.49300 63.06500 52.22750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4345956E-02 -5.2711554E-02 midg,1,midg; midg,igrid,midg 2.5386760E-02 0.1189074 1,midg,midg; igrid,midg,midg -0.4877645 0.6021644 gauss-seidel spectral radius is 0.9991471 estimated iterations to convergence 270 setup time was (sec) 1.100000 now iterating at: 03:15:18 rms-change max change #iterations 9.253846 330.9152 at 10iterations 5.243635 129.1475 at 20iterations 2.948631 70.85271 at 30iterations 1.653145 41.38665 at 40iterations 0.9220718 26.48859 at 50iterations 0.5133976 11.53440 at 60iterations 0.2851616 6.047194 at 70iterations 0.1584770 3.823133 at 80iterations 8.7698705E-02 1.846100 at 90iterations 4.8591673E-02 1.072090 at 100iterations 2.6996031E-02 0.5872202 at 110iterations 1.4877852E-02 0.3745060 at 120iterations 8.2080960E-03 0.1910524 at 130iterations 4.5502223E-03 0.1053810 at 140iterations 2.5136743E-03 5.1303387E-02 at 150iterations 1.3942930E-03 2.9678345E-02 at 160iterations 7.7441824E-04 1.5294075E-02 at 170iterations 4.3276700E-04 8.4228516E-03 at 180iterations finished qdiffx linear iterations at : 03:15:29 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 4.3276700E-04 8.4228516E-03 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 03:15:30 12.484u 0.219s 0:13.02 97.4% 0+0k 0+0io 0pf+0w