Sat Oct 15 11:29:36 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 11:29:36 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 !!! 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 556 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6225518 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): -31.85300 17.84400 ymin,ymax (A): -23.89400 22.68800 zmin,zma (A): -12.39900 44.78500 x,y,z range (A): 49.69700 46.58200 57.18400 scale (grids/A): 0.6225518 object centre (A): -7.004500 -0.6029997 16.19300 number of atom coordinates read : 2590 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.55974 89.27683 89.70075 assigned negative charge : -387.4045 centred at (gu) : 88.43994 89.32804 89.59034 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6599 nv = 96 ne = 84 npr = 53829 no. pairs analyzed = 53829 no. exposed pairs = 2971 no. arc points = 21165 no. surface atoms = 1005 nbur = 1585 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3734 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 0.2100000 number of dielectric boundary points 3148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2112 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8127 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6589412E-09 1.0660051E-08 midg,1,midg; midg,igrid,midg 8.4864604E-09 -1.7780270E-11 1,midg,midg; igrid,midg,midg -7.0481536E-09 8.7884722E-09 gauss-seidel spectral radius is 0.9866329 estimated iterations to convergence 71 setup time was (sec) 0.4500000 now iterating at: 11:29:37 rms-change max change #iterations 0.1306882 21.43411 at 10iterations 1.2028856E-02 1.538746 at 20iterations 1.1303899E-03 0.1709900 at 30iterations 1.0528697E-04 1.4232039E-02 at 40iterations 9.8478085E-06 1.5220642E-03 at 50iterations finished qdiffx linear iterations at : 11:29:40 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 9.8478085E-06 1.5220642E-03 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 11:29:41 3.884u 0.219s 0:04.77 85.7% 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 Sat Oct 15 2011 at 11:29:41 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 !!! 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 556 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.867655 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): -31.85300 17.84400 ymin,ymax (A): -23.89400 22.68800 zmin,zma (A): -12.39900 44.78500 x,y,z range (A): 49.69700 46.58200 57.18400 scale (grids/A): 1.867655 object centre (A): -7.004500 -0.6029997 16.19300 number of atom coordinates read : 2590 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.67857 87.82996 89.10179 assigned negative charge : -387.4045 centred at (gu) : 85.31948 87.98399 88.77090 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21165 grid for indexing accessible points = 1.400000 m= 24909 mr = 50762 m= 3474 mr = 18489 m= 165 mr = 2107 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4207 time to turn everything in is 0.3400000 number of dielectric boundary points 29075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19287 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) : 0.6225518 object centre at (A) : -7.004500 -0.6029997 16.19300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7743498E-02 1.9430924E-02 midg,1,midg; midg,igrid,midg 1.3523867E-02 5.7284194E-03 1,midg,midg; igrid,midg,midg -5.1111295E-03 4.0895309E-02 gauss-seidel spectral radius is 0.9985772 estimated iterations to convergence 210 setup time was (sec) 0.5600000 now iterating at: 11:29:42 rms-change max change #iterations 4.060806 163.7512 at 10iterations 1.871093 63.76881 at 20iterations 0.8615396 26.11481 at 30iterations 0.3968453 13.55443 at 40iterations 0.1833212 5.645037 at 50iterations 8.4601894E-02 2.804304 at 60iterations 3.9021179E-02 1.217281 at 70iterations 1.8039303E-02 0.6041975 at 80iterations 8.3095478E-03 0.2838451 at 90iterations 3.8326499E-03 0.1349030 at 100iterations 1.7648455E-03 6.7104340E-02 at 110iterations 8.1374455E-04 2.6809692E-02 at 120iterations finished qdiffx linear iterations at : 11:29:51 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 8.1374455E-04 2.6809692E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 11:29:52 7.733u 0.215s 0:11.04 71.9% 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 15 2011 at 11:29:52 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 !!! 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 556 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.801483 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): -31.85300 17.84400 ymin,ymax (A): -23.89400 22.68800 zmin,zma (A): -12.39900 44.78500 x,y,z range (A): 49.69700 46.58200 57.18400 scale (grids/A): 2.801483 object centre (A): -7.004500 -0.6029997 16.19300 number of atom coordinates read : 2590 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.51775 86.74484 88.65250 assigned negative charge : -387.4045 centred at (gu) : 82.97916 86.97578 88.15629 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 166737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21165 grid for indexing accessible points = 1.400000 m= 82675 mr = 122899 m= 27652 mr = 68314 m= 5996 mr = 22121 m= 687 mr = 4469 m= 36 mr = 396 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 13393 time to turn everything in is 0.9600000 number of dielectric boundary points 65564 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 19632 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) : 1.867655 object centre at (A) : -7.004500 -0.6029997 16.19300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3437756E-02 0.1847607 midg,1,midg; midg,igrid,midg 0.1602606 6.3005954E-02 1,midg,midg; igrid,midg,midg -3.2436136E-02 0.5577138 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 1.250000 now iterating at: 11:29:54 rms-change max change #iterations 9.524669 287.4869 at 10iterations 5.466994 120.0099 at 20iterations 3.122948 63.03822 at 30iterations 1.782031 34.58730 at 40iterations 1.014772 22.62985 at 50iterations 0.5779372 10.92703 at 60iterations 0.3295642 6.395836 at 70iterations 0.1876283 4.125161 at 80iterations 0.1068718 2.024160 at 90iterations 6.0705524E-02 1.269020 at 100iterations 3.4503769E-02 0.6361885 at 110iterations 1.9659819E-02 0.4117661 at 120iterations 1.1184359E-02 0.2251511 at 130iterations 6.3533876E-03 0.1165199 at 140iterations 3.6195412E-03 6.6349030E-02 at 150iterations 2.0549619E-03 4.0485382E-02 at 160iterations 1.1714153E-03 2.2300720E-02 at 170iterations 6.6496455E-04 1.2392044E-02 at 180iterations finished qdiffx linear iterations at : 11:30:07 total time elapsed so far: 14.35000 # loops : 180 mean,max change (kT/e) : 6.6496455E-04 1.2392044E-02 energy calculations done at 14.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.48000 DelPhi exited at 11:30:07 14.478u 0.299s 0:15.20 97.1% 0+0k 0+0io 0pf+0w