Sat Oct 8 12:36:01 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 Sat Oct 8 2011 at 12:36:01 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6044655 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): -18.12800 23.22900 ymin,ymax (A): -15.99700 32.48900 zmin,zma (A): 18.22900 77.12400 x,y,z range (A): 41.35700 48.48600 58.89500 scale (grids/A): 0.6044655 object centre (A): 2.550500 8.246001 47.67650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000008 assigned positive charge : 316.7017 centred at (gu) : 89.76638 88.94698 88.85078 assigned negative charge : -314.7023 centred at (gu) : 89.71097 89.02197 89.10789 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5697 nv = 96 ne = 84 npr = 49440 no. pairs analyzed = 49440 no. exposed pairs = 3137 no. arc points = 21893 no. surface atoms = 1076 nbur = 1251 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 2753 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.1800000 number of dielectric boundary points 3225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2131 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2145876E-08 -6.2292997E-09 midg,1,midg; midg,igrid,midg 4.3011679E-09 -1.3270491E-09 1,midg,midg; igrid,midg,midg -1.0859192E-09 2.5902396E-09 gauss-seidel spectral radius is 0.9858206 estimated iterations to convergence 69 setup time was (sec) 0.3900000 now iterating at: 12:36:01 rms-change max change #iterations 9.6956037E-02 16.48475 at 10iterations 9.6585546E-03 1.800224 at 20iterations 2.0488366E-03 0.4169998 at 30iterations 7.6491619E-04 0.1595421 at 40iterations 3.0302029E-04 6.3224792E-02 at 50iterations finished qdiffx linear iterations at : 12:36:04 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 3.0302029E-04 6.3224792E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 12:36:05 3.623u 0.219s 0:04.12 92.9% 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 8 2011 at 12:36:05 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.813397 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): -18.12800 23.22900 ymin,ymax (A): -15.99700 32.48900 zmin,zma (A): 18.22900 77.12400 x,y,z range (A): 41.35700 48.48600 58.89500 scale (grids/A): 1.813397 object centre (A): 2.550500 8.246001 47.67650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000008 assigned positive charge : 316.7017 centred at (gu) : 89.29884 86.84085 86.55211 assigned negative charge : -314.7023 centred at (gu) : 89.13321 87.06599 87.32383 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 61714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21893 grid for indexing accessible points = 1.400000 m= 20203 mr = 40102 m= 2960 mr = 13584 m= 128 mr = 1604 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 567 time to turn everything in is 0.3200000 number of dielectric boundary points 29687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 17193 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) : 0.6044655 object centre at (A) : 2.550500 8.246001 47.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1224045E-02 -2.0558160E-02 midg,1,midg; midg,igrid,midg 3.0224868E-03 -1.1271844E-03 1,midg,midg; igrid,midg,midg -1.4774203E-03 6.5104598E-03 gauss-seidel spectral radius is 0.9984783 estimated iterations to convergence 203 setup time was (sec) 0.5600000 now iterating at: 12:36:06 rms-change max change #iterations 3.418609 184.1974 at 10iterations 1.529942 55.55088 at 20iterations 0.6837920 27.50162 at 30iterations 0.3067648 12.30599 at 40iterations 0.1379589 4.650497 at 50iterations 6.2469717E-02 2.220912 at 60iterations 2.8198870E-02 1.067781 at 70iterations 1.3125753E-02 0.5182343 at 80iterations 6.3794092E-03 0.2643509 at 90iterations 3.3926936E-03 0.1469383 at 100iterations 2.0261202E-03 9.0930939E-02 at 110iterations 1.3534825E-03 5.8361053E-02 at 120iterations finished qdiffx linear iterations at : 12:36:13 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 1.3534825E-03 5.8361053E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 12:36:14 8.380u 0.248s 0:08.92 96.6% 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 8 2011 at 12:36:14 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.720095 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): -18.12800 23.22900 ymin,ymax (A): -15.99700 32.48900 zmin,zma (A): 18.22900 77.12400 x,y,z range (A): 41.35700 48.48600 58.89500 scale (grids/A): 2.720095 object centre (A): 2.550500 8.246001 47.67650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000008 assigned positive charge : 316.7017 centred at (gu) : 88.94813 85.26111 84.82811 assigned negative charge : -314.7023 centred at (gu) : 88.69987 85.59901 85.98584 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 143054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21893 grid for indexing accessible points = 1.400000 m= 66180 mr = 98690 m= 22684 mr = 51167 m= 4906 mr = 16990 m= 532 mr = 3325 m= 24 mr = 301 m= 0 mr = 5 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1943 time to turn everything in is 0.8000000 number of dielectric boundary points 66902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 17541 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) : 1.813397 object centre at (A) : 2.550500 8.246001 47.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6341104 -0.2571391 midg,1,midg; midg,igrid,midg 1.9960809E-02 -9.1220979E-03 1,midg,midg; igrid,midg,midg -2.4680980E-02 5.8113951E-02 gauss-seidel spectral radius is 0.9992160 estimated iterations to convergence 282 setup time was (sec) 1.050000 now iterating at: 12:36:15 rms-change max change #iterations 8.327435 339.2626 at 10iterations 4.778758 168.5466 at 20iterations 2.730359 58.34081 at 30iterations 1.554484 37.40894 at 40iterations 0.8832653 19.30710 at 50iterations 0.5015916 13.38590 at 60iterations 0.2842931 6.687672 at 70iterations 0.1612341 3.237510 at 80iterations 9.1487952E-02 1.764799 at 90iterations 5.1762875E-02 1.141106 at 100iterations 2.9288696E-02 0.6405449 at 110iterations 1.6627463E-02 0.3331480 at 120iterations 9.4890958E-03 0.2221069 at 130iterations 5.4550264E-03 0.1157265 at 140iterations 3.1910755E-03 7.7289581E-02 at 150iterations 1.9341740E-03 4.3460846E-02 at 160iterations 1.2383417E-03 2.9632568E-02 at 170iterations 8.5696304E-04 2.1682739E-02 at 180iterations finished qdiffx linear iterations at : 12:36:28 total time elapsed so far: 13.47000 # loops : 180 mean,max change (kT/e) : 8.5696304E-04 2.1682739E-02 energy calculations done at 13.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.60000 DelPhi exited at 12:36:28 13.604u 0.264s 0:14.15 97.9% 0+0k 0+0io 0pf+0w