Sun Oct 9 16:33:09 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 Sun Oct 9 2011 at 16:33:09 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2313 !!! WARNING: GLM 570 has a net charge of -0.0940 !!! WARNING: GLM 642 has a net charge of -0.0940 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: 0.5752327 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): -25.68800 27.92100 ymin,ymax (A): -16.33600 45.55200 zmin,zma (A): -25.86500 25.17100 x,y,z range (A): 53.60900 61.88800 51.03600 scale (grids/A): 0.5752327 object centre (A): 1.116500 14.60800 -0.3470001 number of atom coordinates read : 2313 total number of charged atoms : 2168 net assigned charge : 0.3120032 assigned positive charge : 337.4591 centred at (gu) : 90.82093 92.39684 90.66555 assigned negative charge : -337.1479 centred at (gu) : 90.64922 92.23658 90.68128 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5057 nv = 96 ne = 84 npr = 46183 no. pairs analyzed = 46183 no. exposed pairs = 3137 no. arc points = 22113 no. surface atoms = 1066 nbur = 1247 mkacc time = 8.0000006E-02 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 = 1.484000 m= 211 mr = 2433 m= 0 mr = 3 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2218 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7246454E-10 -2.8596550E-10 midg,1,midg; midg,igrid,midg -1.3197046E-09 3.9462726E-09 1,midg,midg; igrid,midg,midg -2.0529207E-09 2.8739955E-09 gauss-seidel spectral radius is 0.9843564 estimated iterations to convergence 66 setup time was (sec) 0.3700000 now iterating at: 16:33:09 rms-change max change #iterations 7.6787271E-02 14.26557 at 10iterations 5.8515575E-03 1.056706 at 20iterations 4.5634017E-04 7.5523376E-02 at 30iterations 3.4434397E-05 7.3037148E-03 at 40iterations 3.0241747E-06 5.3215027E-04 at 50iterations finished qdiffx linear iterations at : 16:33:12 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 3.0241747E-06 5.3215027E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 16:33:13 3.401u 0.179s 0:03.93 90.8% 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 Sun Oct 9 2011 at 16:33:13 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2313 !!! WARNING: GLM 570 has a net charge of -0.0940 !!! WARNING: GLM 642 has a net charge of -0.0940 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: 1.725698 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): -25.68800 27.92100 ymin,ymax (A): -16.33600 45.55200 zmin,zma (A): -25.86500 25.17100 x,y,z range (A): 53.60900 61.88800 51.03600 scale (grids/A): 1.725698 object centre (A): 1.116500 14.60800 -0.3470001 number of atom coordinates read : 2313 total number of charged atoms : 2168 net assigned charge : 0.3120032 assigned positive charge : 337.4591 centred at (gu) : 92.46225 97.19006 91.99648 assigned negative charge : -337.1479 centred at (gu) : 91.94765 96.70972 92.04388 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 55620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22113 grid for indexing accessible points = 1.400000 m= 16615 mr = 35946 m= 1918 mr = 11038 m= 59 mr = 982 m= 0 mr = 6 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 292 time to turn everything in is 0.2900000 number of dielectric boundary points 26240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 16815 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) : 0.5752327 object centre at (A) : 1.116500 14.60800 -0.3470001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2721763E-03 -5.4303687E-03 midg,1,midg; midg,igrid,midg -5.4135937E-03 -1.9602228E-02 1,midg,midg; igrid,midg,midg -5.7105161E-03 2.1832665E-02 gauss-seidel spectral radius is 0.9983152 estimated iterations to convergence 193 setup time was (sec) 0.5100000 now iterating at: 16:33:13 rms-change max change #iterations 3.207554 164.7912 at 10iterations 1.366959 50.76303 at 20iterations 0.5872257 21.88575 at 30iterations 0.2520296 10.52456 at 40iterations 0.1086014 4.279638 at 50iterations 4.6695072E-02 1.830512 at 60iterations 2.0031199E-02 0.7564458 at 70iterations 8.6103603E-03 0.3249068 at 80iterations 3.6977774E-03 0.1502819 at 90iterations 1.5917153E-03 6.4472198E-02 at 100iterations 6.8502745E-04 2.4120331E-02 at 110iterations 2.9564986E-04 1.1693716E-02 at 120iterations finished qdiffx linear iterations at : 16:33:20 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.9564986E-04 1.1693716E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 16:33:21 7.708u 0.192s 0:08.24 95.7% 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 Sun Oct 9 2011 at 16:33:21 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2313 !!! WARNING: GLM 570 has a net charge of -0.0940 !!! WARNING: GLM 642 has a net charge of -0.0940 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: 2.588547 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): -25.68800 27.92100 ymin,ymax (A): -16.33600 45.55200 zmin,zma (A): -25.86500 25.17100 x,y,z range (A): 53.60900 61.88800 51.03600 scale (grids/A): 2.588547 object centre (A): 1.116500 14.60800 -0.3470001 number of atom coordinates read : 2313 total number of charged atoms : 2168 net assigned charge : 0.3120032 assigned positive charge : 337.4591 centred at (gu) : 93.69331 100.7848 92.99458 assigned negative charge : -337.1479 centred at (gu) : 92.92150 100.0644 93.06576 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 129066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22113 grid for indexing accessible points = 1.400000 m= 56581 mr = 88463 m= 16717 mr = 43371 m= 3077 mr = 12480 m= 266 mr = 2112 m= 9 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 931 time to turn everything in is 0.6800000 number of dielectric boundary points 59143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17333 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) : 1.725698 object centre at (A) : 1.116500 14.60800 -0.3470001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9996187E-02 -5.3338863E-02 midg,1,midg; midg,igrid,midg -5.8844630E-02 -0.5708975 1,midg,midg; igrid,midg,midg -7.2013862E-02 0.2956120 gauss-seidel spectral radius is 0.9991694 estimated iterations to convergence 274 setup time was (sec) 0.9100000 now iterating at: 16:33:22 rms-change max change #iterations 8.080941 275.7693 at 10iterations 4.583766 137.2090 at 20iterations 2.595034 62.82505 at 30iterations 1.457311 38.46539 at 40iterations 0.8200026 21.47198 at 50iterations 0.4591094 10.55645 at 60iterations 0.2566828 6.315581 at 70iterations 0.1429811 3.242378 at 80iterations 7.9726644E-02 1.917665 at 90iterations 4.4436853E-02 1.008263 at 100iterations 2.4751524E-02 0.5015764 at 110iterations 1.3755728E-02 0.3688517 at 120iterations 7.6554473E-03 0.1703166 at 130iterations 4.2545889E-03 9.4635010E-02 at 140iterations 2.3648289E-03 5.3108215E-02 at 150iterations 1.3149619E-03 3.1736851E-02 at 160iterations 7.3198171E-04 1.7944336E-02 at 170iterations 4.0610632E-04 9.3994141E-03 at 180iterations finished qdiffx linear iterations at : 16:33:33 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 4.0610632E-04 9.3994141E-03 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 16:33:34 12.310u 0.221s 0:12.79 97.9% 0+0k 0+0io 0pf+0w