Sat Oct 8 19:59:12 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 19:59:12 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 531 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6192597 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): -31.28600 17.45100 ymin,ymax (A): -23.50300 22.69600 zmin,zma (A): -12.39100 45.09700 x,y,z range (A): 48.73700 46.19900 57.48800 scale (grids/A): 0.6192597 object centre (A): -6.917500 -0.4035006 16.35300 number of atom coordinates read : 2586 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 88.52788 89.22042 89.53361 assigned negative charge : -390.4956 centred at (gu) : 88.41296 89.28160 89.41408 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6361 nv = 96 ne = 84 npr = 53832 no. pairs analyzed = 53832 no. exposed pairs = 3051 no. arc points = 21669 no. surface atoms = 1021 nbur = 1565 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 3494 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.2900000 number of dielectric boundary points 3144 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2184 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8038 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7227369E-09 1.0255452E-08 midg,1,midg; midg,igrid,midg 9.0669054E-09 -2.6380390E-10 1,midg,midg; igrid,midg,midg -5.5673723E-09 8.0216536E-09 gauss-seidel spectral radius is 0.9864901 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 19:59:12 rms-change max change #iterations 0.1263841 18.52966 at 10iterations 1.1533590E-02 1.582355 at 20iterations 1.0579284E-03 0.1522522 at 30iterations 1.0232232E-04 1.4499664E-02 at 40iterations 9.3675226E-06 1.5525818E-03 at 50iterations finished qdiffx linear iterations at : 19:59:15 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 9.3675226E-06 1.5525818E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 19:59:15 3.165u 0.154s 0:03.60 91.9% 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 19:59:15 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 531 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.857779 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): -31.28600 17.45100 ymin,ymax (A): -23.50300 22.69600 zmin,zma (A): -12.39100 45.09700 x,y,z range (A): 48.73700 46.19900 57.48800 scale (grids/A): 1.857779 object centre (A): -6.917500 -0.4035006 16.35300 number of atom coordinates read : 2586 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 85.58310 87.66090 88.59992 assigned negative charge : -390.4956 centred at (gu) : 85.23883 87.84457 88.24223 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21669 grid for indexing accessible points = 1.400000 m= 23582 mr = 48380 m= 3290 mr = 17289 m= 141 mr = 1957 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 4097 time to turn everything in is 0.4800000 number of dielectric boundary points 29061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19333 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) : 0.6192597 object centre at (A) : -6.917500 -0.4035006 16.35300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7211705E-02 3.2246288E-02 midg,1,midg; midg,igrid,midg 1.2015537E-02 5.4771453E-04 1,midg,midg; igrid,midg,midg -4.7864770E-03 3.6078185E-02 gauss-seidel spectral radius is 0.9985615 estimated iterations to convergence 209 setup time was (sec) 0.7500000 now iterating at: 19:59:16 rms-change max change #iterations 4.042038 163.7132 at 10iterations 1.858671 64.10972 at 20iterations 0.8489734 33.42638 at 30iterations 0.3903491 14.77439 at 40iterations 0.1790403 5.419073 at 50iterations 8.2347900E-02 2.752594 at 60iterations 3.7719764E-02 1.257001 at 70iterations 1.7316267E-02 0.5847750 at 80iterations 7.9525840E-03 0.2988873 at 90iterations 3.6600856E-03 0.1165638 at 100iterations 1.6787136E-03 5.7647705E-02 at 110iterations 7.7237166E-04 2.5069237E-02 at 120iterations finished qdiffx linear iterations at : 19:59:22 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 7.7237166E-04 2.5069237E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 19:59:23 6.980u 0.185s 0:07.44 96.2% 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 8 2011 at 19:59:23 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 531 has a net charge of 1.4000 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: 2.786669 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): -31.28600 17.45100 ymin,ymax (A): -23.50300 22.69600 zmin,zma (A): -12.39100 45.09700 x,y,z range (A): 48.73700 46.19900 57.48800 scale (grids/A): 2.786669 object centre (A): -6.917500 -0.4035006 16.35300 number of atom coordinates read : 2586 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 83.37462 86.49118 87.89997 assigned negative charge : -390.4956 centred at (gu) : 82.85812 86.76678 87.36327 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 161611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21669 grid for indexing accessible points = 1.400000 m= 78558 mr = 117493 m= 25954 mr = 64085 m= 5645 mr = 20741 m= 694 mr = 4186 m= 32 mr = 426 m= 0 mr = 8 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 13735 time to turn everything in is 1.180000 number of dielectric boundary points 65555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 19726 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) : 1.857779 object centre at (A) : -6.917500 -0.4035006 16.35300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2870995E-02 0.4010459 midg,1,midg; midg,igrid,midg 0.1510419 -7.3293857E-03 1,midg,midg; igrid,midg,midg -4.5486350E-02 0.4751391 gauss-seidel spectral radius is 0.9992335 estimated iterations to convergence 285 setup time was (sec) 1.460000 now iterating at: 19:59:25 rms-change max change #iterations 9.491048 334.0423 at 10iterations 5.458837 117.3807 at 20iterations 3.115087 79.37194 at 30iterations 1.775854 46.71170 at 40iterations 1.013103 19.43663 at 50iterations 0.5770761 11.22063 at 60iterations 0.3288139 7.297337 at 70iterations 0.1865924 3.495929 at 80iterations 0.1061368 2.039152 at 90iterations 6.0506117E-02 1.286921 at 100iterations 3.4405231E-02 0.6328411 at 110iterations 1.9593025E-02 0.3759842 at 120iterations 1.1149990E-02 0.2529793 at 130iterations 6.3292976E-03 0.1291552 at 140iterations 3.6023897E-03 6.8874359E-02 at 150iterations 2.0493527E-03 3.8530350E-02 at 160iterations 1.1712536E-03 2.1683216E-02 at 170iterations 6.6775951E-04 1.2619019E-02 at 180iterations finished qdiffx linear iterations at : 19:59:34 total time elapsed so far: 11.06000 # loops : 180 mean,max change (kT/e) : 6.6775951E-04 1.2619019E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.23000 DelPhi exited at 19:59:35 11.235u 0.206s 0:11.81 96.7% 0+0k 0+0io 0pf+0w