Tue Oct 11 08:34:13 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 Tue Oct 11 2011 at 08:34:13 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6622147 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): -8.274000 40.59400 ymin,ymax (A): -26.28700 22.22900 zmin,zma (A): -9.873000 43.88600 x,y,z range (A): 48.86800 48.51600 53.75900 scale (grids/A): 0.6622147 object centre (A): 16.16000 -2.028999 17.00650 number of atom coordinates read : 2708 total number of charged atoms : 2556 net assigned charge : 2.154016 assigned positive charge : 412.3829 centred at (gu) : 89.59277 90.17873 88.65813 assigned negative charge : -410.2293 centred at (gu) : 89.90110 90.01392 88.62878 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7867 nv = 96 ne = 84 npr = 55770 no. pairs analyzed = 55770 no. exposed pairs = 3324 no. arc points = 23042 no. surface atoms = 1121 nbur = 1587 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4450 m= 4 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3300000 number of dielectric boundary points 3807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2286 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2443453E-09 9.2228909E-09 midg,1,midg; midg,igrid,midg -3.0215901E-08 4.3043723E-08 1,midg,midg; igrid,midg,midg 7.8050441E-08 -5.9367611E-08 gauss-seidel spectral radius is 0.9881868 estimated iterations to convergence 75 setup time was (sec) 0.6100000 now iterating at: 08:34:14 rms-change max change #iterations 0.1776838 22.77731 at 10iterations 1.9623574E-02 2.599137 at 20iterations 2.1311364E-03 0.2823982 at 30iterations 2.5415735E-04 3.1555176E-02 at 40iterations 4.0235980E-05 6.3648224E-03 at 50iterations finished qdiffx linear iterations at : 08:34:18 total time elapsed so far: 4.950000 # loops : 50 mean,max change (kT/e) : 4.0235980E-05 6.3648224E-03 energy calculations done at 4.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.120000 DelPhi exited at 08:34:18 5.124u 0.378s 0:05.79 94.8% 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 08:34:18 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.986644 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): -8.274000 40.59400 ymin,ymax (A): -26.28700 22.22900 zmin,zma (A): -9.873000 43.88600 x,y,z range (A): 48.86800 48.51600 53.75900 scale (grids/A): 1.986644 object centre (A): 16.16000 -2.028999 17.00650 number of atom coordinates read : 2708 total number of charged atoms : 2556 net assigned charge : 2.154016 assigned positive charge : 412.3829 centred at (gu) : 88.77744 90.53567 85.97398 assigned negative charge : -410.2293 centred at (gu) : 89.70319 90.04135 85.88609 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 84934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23042 grid for indexing accessible points = 1.400000 m= 31848 mr = 60064 m= 5467 mr = 23657 m= 415 mr = 3502 m= 6 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 599 time to turn everything in is 0.7100000 number of dielectric boundary points 35289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 20147 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) : 0.6622147 object centre at (A) : 16.16000 -2.028999 17.00650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6225965E-02 -2.9092235E-02 midg,1,midg; midg,igrid,midg -1.5079272E-02 4.3199454E-02 1,midg,midg; igrid,midg,midg 9.0377063E-02 -1.3958333E-02 gauss-seidel spectral radius is 0.9987506 estimated iterations to convergence 224 setup time was (sec) 1.010000 now iterating at: 08:34:36 rms-change max change #iterations 4.801991 212.2182 at 10iterations 2.335480 74.15312 at 20iterations 1.127439 43.22455 at 30iterations 0.5470852 16.48332 at 40iterations 0.2658166 7.903008 at 50iterations 0.1287021 3.976846 at 60iterations 6.2287211E-02 1.877600 at 70iterations 3.0278498E-02 0.8265533 at 80iterations 1.4692869E-02 0.4500618 at 90iterations 7.1220798E-03 0.2109070 at 100iterations 3.4693356E-03 9.9644661E-02 at 110iterations 1.6894955E-03 5.0426483E-02 at 120iterations finished qdiffx linear iterations at : 08:34:46 total time elapsed so far: 11.48000 # loops : 120 mean,max change (kT/e) : 1.6894955E-03 5.0426483E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.66000 DelPhi exited at 08:34:47 11.668u 0.469s 0:28.56 42.4% 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 08:34:47 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.979966 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): -8.274000 40.59400 ymin,ymax (A): -26.28700 22.22900 zmin,zma (A): -9.873000 43.88600 x,y,z range (A): 48.86800 48.51600 53.75900 scale (grids/A): 2.979966 object centre (A): 16.16000 -2.028999 17.00650 number of atom coordinates read : 2708 total number of charged atoms : 2556 net assigned charge : 2.154016 assigned positive charge : 412.3829 centred at (gu) : 88.16625 90.80353 83.96091 assigned negative charge : -410.2293 centred at (gu) : 89.55477 90.06196 83.82895 start vw surface at 0.1300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 196443 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23042 grid for indexing accessible points = 1.400000 m= 102113 mr = 145075 m= 38161 mr = 84268 m= 10003 mr = 30837 m= 1656 mr = 7614 m= 116 mr = 1096 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 1987 time to turn everything in is 1.870000 number of dielectric boundary points 79555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 20443 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) : 1.986644 object centre at (A) : 16.16000 -2.028999 17.00650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1558450 -0.3521895 midg,1,midg; midg,igrid,midg -0.1424999 0.4919357 1,midg,midg; igrid,midg,midg 0.7755611 -9.3421280E-02 gauss-seidel spectral radius is 0.9992872 estimated iterations to convergence 296 setup time was (sec) 2.230000 now iterating at: 08:34:51 rms-change max change #iterations 11.01033 383.0683 at 10iterations 6.470201 137.1481 at 20iterations 3.803208 76.86388 at 30iterations 2.226232 38.21957 at 40iterations 1.305090 26.71787 at 50iterations 0.7641366 14.68464 at 60iterations 0.4458438 7.513004 at 70iterations 0.2595910 4.710693 at 80iterations 0.1518099 2.749786 at 90iterations 8.8350378E-02 1.453424 at 100iterations 5.1442370E-02 0.8812790 at 110iterations 3.0007049E-02 0.4894810 at 120iterations 1.7480627E-02 0.2814932 at 130iterations 1.0191948E-02 0.1845932 at 140iterations 5.9646657E-03 0.1084385 at 150iterations 3.5016744E-03 6.1113358E-02 at 160iterations 2.0651708E-03 3.4416199E-02 at 170iterations 1.2294255E-03 2.0885468E-02 at 180iterations finished qdiffx linear iterations at : 08:35:09 total time elapsed so far: 20.57000 # loops : 180 mean,max change (kT/e) : 1.2294255E-03 2.0885468E-02 energy calculations done at 20.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.73000 DelPhi exited at 08:35:10 20.734u 0.468s 0:22.72 93.2% 0+0k 0+0io 0pf+0w