Sat Oct 15 14:36:44 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 14:36:44 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 = 2899 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: 0.5920506 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): -27.26100 32.46000 ymin,ymax (A): -7.544000 40.05500 zmin,zma (A): 3.730000 63.86000 x,y,z range (A): 59.72100 47.59900 60.13000 scale (grids/A): 0.5920506 object centre (A): 2.599500 16.25550 33.79500 number of atom coordinates read : 2899 total number of charged atoms : 2758 net assigned charge : -2.999964 assigned positive charge : 434.5101 centred at (gu) : 90.89860 89.58389 91.01814 assigned negative charge : -437.5112 centred at (gu) : 91.00889 89.46291 91.08273 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6910 nv = 96 ne = 84 npr = 57099 no. pairs analyzed = 57099 no. exposed pairs = 3845 no. arc points = 27955 no. surface atoms = 1296 nbur = 1603 mkacc time = 0.1500000 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 = 1.456000 m= 331 mr = 3530 m= 0 mr = 16 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3100000 number of dielectric boundary points 3695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2845 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8606 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9462548E-10 -3.7795447E-09 midg,1,midg; midg,igrid,midg -5.3181104E-09 2.6360205E-09 1,midg,midg; igrid,midg,midg 2.0824948E-09 -5.5189515E-09 gauss-seidel spectral radius is 0.9852754 estimated iterations to convergence 68 setup time was (sec) 0.6000000 now iterating at: 14:36:45 rms-change max change #iterations 0.1036883 16.26305 at 10iterations 8.4918616E-03 1.189928 at 20iterations 7.0146273E-04 0.1150742 at 30iterations 5.7485129E-05 8.3618164E-03 at 40iterations 4.7893532E-06 8.0680847E-04 at 50iterations finished qdiffx linear iterations at : 14:36:50 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 4.7893532E-06 8.0680847E-04 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 14:36:51 4.091u 0.469s 0:06.64 68.5% 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 14:36:51 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 = 2899 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: 1.776152 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): -27.26100 32.46000 ymin,ymax (A): -7.544000 40.05500 zmin,zma (A): 3.730000 63.86000 x,y,z range (A): 59.72100 47.59900 60.13000 scale (grids/A): 1.776152 object centre (A): 2.599500 16.25550 33.79500 number of atom coordinates read : 2899 total number of charged atoms : 2758 net assigned charge : -2.999964 assigned positive charge : 434.5101 centred at (gu) : 92.69497 88.75089 93.05382 assigned negative charge : -437.5112 centred at (gu) : 93.02615 88.38821 93.24797 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27955 grid for indexing accessible points = 1.400000 m= 24930 mr = 49923 m= 3128 mr = 17468 m= 143 mr = 1592 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 346 time to turn everything in is 0.6000000 number of dielectric boundary points 34257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 21460 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) : 0.5920506 object centre at (A) : 2.599500 16.25550 33.79500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0085238E-02 1.6495988E-02 midg,1,midg; midg,igrid,midg -1.7548360E-02 5.4001804E-03 1,midg,midg; igrid,midg,midg 2.5104094E-02 -5.3248942E-02 gauss-seidel spectral radius is 0.9984771 estimated iterations to convergence 203 setup time was (sec) 0.8900000 now iterating at: 14:36:53 rms-change max change #iterations 3.962222 199.4849 at 10iterations 1.755136 59.91694 at 20iterations 0.7848665 26.94315 at 30iterations 0.3514365 11.70755 at 40iterations 0.1581944 5.550297 at 50iterations 7.0396416E-02 2.434288 at 60iterations 3.1645324E-02 1.100091 at 70iterations 1.4110772E-02 0.4821472 at 80iterations 6.3670571E-03 0.2075443 at 90iterations 2.8511544E-03 0.1041946 at 100iterations 1.2765273E-03 4.2284369E-02 at 110iterations 5.7310809E-04 2.1386623E-02 at 120iterations finished qdiffx linear iterations at : 14:37:06 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 5.7310809E-04 2.1386623E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 14:37:07 9.598u 0.470s 0:16.17 62.2% 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 14:37:08 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 = 2899 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: 2.664227 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): -27.26100 32.46000 ymin,ymax (A): -7.544000 40.05500 zmin,zma (A): 3.730000 63.86000 x,y,z range (A): 59.72100 47.59900 60.13000 scale (grids/A): 2.664227 object centre (A): 2.599500 16.25550 33.79500 number of atom coordinates read : 2899 total number of charged atoms : 2758 net assigned charge : -2.999964 assigned positive charge : 434.5101 centred at (gu) : 94.04233 88.12629 94.58059 assigned negative charge : -437.5112 centred at (gu) : 94.53917 87.58216 94.87198 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 173861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27955 grid for indexing accessible points = 1.400000 m= 83000 mr = 122256 m= 26977 mr = 65820 m= 5227 mr = 20675 m= 543 mr = 3399 m= 26 mr = 315 m= 0 mr = 3 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1144 time to turn everything in is 1.530000 number of dielectric boundary points 77166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 22061 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) : 1.776152 object centre at (A) : 2.599500 16.25550 33.79500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4990769 0.3312795 midg,1,midg; midg,igrid,midg -0.1983273 7.2030626E-02 1,midg,midg; igrid,midg,midg 0.4003731 -0.6708889 gauss-seidel spectral radius is 0.9992359 estimated iterations to convergence 286 setup time was (sec) 1.850000 now iterating at: 14:37:14 rms-change max change #iterations 9.769913 316.0826 at 10iterations 5.735556 158.2739 at 20iterations 3.324065 119.3501 at 30iterations 1.923039 42.45463 at 40iterations 1.106068 22.09628 at 50iterations 0.6351103 13.90392 at 60iterations 0.3638788 7.744044 at 70iterations 0.2080801 4.312020 at 80iterations 0.1189170 2.474563 at 90iterations 6.7917138E-02 1.306080 at 100iterations 3.8660210E-02 0.7369919 at 110iterations 2.2043725E-02 0.4662247 at 120iterations 1.2556737E-02 0.2264872 at 130iterations 7.1573257E-03 0.1427822 at 140iterations 4.0771109E-03 7.8472137E-02 at 150iterations 2.3198491E-03 4.4037864E-02 at 160iterations 1.3178496E-03 2.4137735E-02 at 170iterations 7.5159234E-04 1.3816833E-02 at 180iterations finished qdiffx linear iterations at : 14:37:49 total time elapsed so far: 16.89000 # loops : 180 mean,max change (kT/e) : 7.5159234E-04 1.3816833E-02 energy calculations done at 16.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.07000 DelPhi exited at 14:37:52 17.078u 0.515s 0:44.61 39.4% 0+0k 0+0io 0pf+0w