Mon Oct 10 14:06:00 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 Mon Oct 10 2011 at 14:06:00 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: HIZ 44 has a net charge of 0.2000 !!! WARNING: SEP 106 has a net charge of -0.4750 !!! WARNING: GLM 424 has a net charge of -0.6000 !!! WARNING: SEP 733 has a net charge of -0.4750 !!! WARNING: ZN7 778 has a net charge of 1.4000 !!! WARNING: ZN7 782 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4983133 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): 25.80700 97.24800 ymin,ymax (A): -0.7270000 63.88400 zmin,zma (A): 15.54700 72.05900 x,y,z range (A): 71.44100 64.61100 56.51200 scale (grids/A): 0.4983133 object centre (A): 61.52750 31.57850 43.80300 number of atom coordinates read : 4556 total number of charged atoms : 4391 net assigned charge : 10.35004 assigned positive charge : 694.4335 centred at (gu) : 89.87320 89.17519 89.60015 assigned negative charge : -684.0885 centred at (gu) : 89.79485 89.02154 89.50533 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7162 nv = 96 ne = 84 npr = 89343 no. pairs analyzed = 89343 no. exposed pairs = 5949 no. arc points = 42264 no. surface atoms = 1992 nbur = 2564 mkacc time = 0.2300000 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 = 1.736000 m= 260 mr = 3511 m= 0 mr = 5 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4143 ## 708 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9794 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8911660E-11 1.9991447E-10 midg,1,midg; midg,igrid,midg -1.7750958E-10 2.4431521E-10 1,midg,midg; igrid,midg,midg -2.9043285E-11 1.9257700E-10 gauss-seidel spectral radius is 0.9794023 estimated iterations to convergence 58 setup time was (sec) 0.7500000 now iterating at: 14:06:01 rms-change max change #iterations 5.6586981E-02 10.43816 at 10iterations 2.9941492E-03 0.5097809 at 20iterations 1.9984401E-04 3.4279823E-02 at 30iterations 4.0789608E-05 1.0725856E-02 at 40iterations 1.3204819E-05 3.6674738E-03 at 50iterations finished qdiffx linear iterations at : 14:06:05 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 1.3204819E-05 3.6674738E-03 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.850000 DelPhi exited at 14:06:06 4.854u 0.394s 0:05.60 93.5% 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 Mon Oct 10 2011 at 14:06:06 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: HIZ 44 has a net charge of 0.2000 !!! WARNING: SEP 106 has a net charge of -0.4750 !!! WARNING: GLM 424 has a net charge of -0.6000 !!! WARNING: SEP 733 has a net charge of -0.4750 !!! WARNING: ZN7 778 has a net charge of 1.4000 !!! WARNING: ZN7 782 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.494940 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): 25.80700 97.24800 ymin,ymax (A): -0.7270000 63.88400 zmin,zma (A): 15.54700 72.05900 x,y,z range (A): 71.44100 64.61100 56.51200 scale (grids/A): 1.494940 object centre (A): 61.52750 31.57850 43.80300 number of atom coordinates read : 4556 total number of charged atoms : 4391 net assigned charge : 10.35004 assigned positive charge : 694.4335 centred at (gu) : 89.61839 87.52380 88.79859 assigned negative charge : -684.0885 centred at (gu) : 89.38385 87.06414 88.51588 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42264 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 21593 mr = 53619 m= 1676 mr = 13791 m= 40 mr = 658 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 354 time to turn everything in is 0.6800000 number of dielectric boundary points 36344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 688 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 32703 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) : 0.4983133 object centre at (A) : 61.52750 31.57850 43.80300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6604178E-03 1.6509520E-03 midg,1,midg; midg,igrid,midg 1.9747825E-02 1.9169781E-02 1,midg,midg; igrid,midg,midg 3.4168307E-03 1.1087407E-02 gauss-seidel spectral radius is 0.9979956 estimated iterations to convergence 178 setup time was (sec) 0.9800000 now iterating at: 14:06:07 rms-change max change #iterations 3.459451 162.1567 at 10iterations 1.374401 50.60302 at 20iterations 0.5442856 19.65002 at 30iterations 0.2169113 7.200710 at 40iterations 8.6636648E-02 3.307239 at 50iterations 3.4545805E-02 1.175060 at 60iterations 1.3757142E-02 0.4609222 at 70iterations 5.5179549E-03 0.1922073 at 80iterations 2.2093642E-03 7.6323032E-02 at 90iterations 8.8983501E-04 3.3706665E-02 at 100iterations 3.6533712E-04 1.3626099E-02 at 110iterations 1.5745891E-04 6.5362453E-03 at 120iterations finished qdiffx linear iterations at : 14:06:18 total time elapsed so far: 11.57000 # loops : 120 mean,max change (kT/e) : 1.5745891E-04 6.5362453E-03 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.74000 DelPhi exited at 14:06:18 11.747u 0.428s 0:12.64 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 Mon Oct 10 2011 at 14:06:18 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: HIZ 44 has a net charge of 0.2000 !!! WARNING: SEP 106 has a net charge of -0.4750 !!! WARNING: GLM 424 has a net charge of -0.6000 !!! WARNING: SEP 733 has a net charge of -0.4750 !!! WARNING: ZN7 778 has a net charge of 1.4000 !!! WARNING: ZN7 782 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.242410 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): 25.80700 97.24800 ymin,ymax (A): -0.7270000 63.88400 zmin,zma (A): 15.54700 72.05900 x,y,z range (A): 71.44100 64.61100 56.51200 scale (grids/A): 2.242410 object centre (A): 61.52750 31.57850 43.80300 number of atom coordinates read : 4556 total number of charged atoms : 4391 net assigned charge : 10.35004 assigned positive charge : 694.4335 centred at (gu) : 89.42721 86.28526 88.19754 assigned negative charge : -684.0885 centred at (gu) : 89.07573 85.59607 87.77355 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 189329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42264 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 78662 mr = 132756 m= 18144 mr = 59890 m= 2200 mr = 12465 m= 97 mr = 1270 m= 0 mr = 20 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 1180 time to turn everything in is 1.640000 number of dielectric boundary points 82031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 35005 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) : 1.494940 object centre at (A) : 61.52750 31.57850 43.80300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1250942 9.9203037E-03 midg,1,midg; midg,igrid,midg 0.5135405 0.3281411 1,midg,midg; igrid,midg,midg 0.2354437 0.3084073 gauss-seidel spectral radius is 0.9991258 estimated iterations to convergence 267 setup time was (sec) 2.050000 now iterating at: 14:06:21 rms-change max change #iterations 9.743105 283.1384 at 10iterations 5.586951 181.7630 at 20iterations 3.166503 77.92426 at 30iterations 1.777684 49.77968 at 40iterations 0.9921663 22.12637 at 50iterations 0.5523452 12.37890 at 60iterations 0.3066216 6.279381 at 70iterations 0.1696136 3.160216 at 80iterations 9.3573026E-02 1.959161 at 90iterations 5.1644839E-02 1.067019 at 100iterations 2.8425695E-02 0.5622692 at 110iterations 1.5618119E-02 0.3384132 at 120iterations 8.6278459E-03 0.1834602 at 130iterations 4.7474499E-03 9.4818115E-02 at 140iterations 2.6100012E-03 5.2249908E-02 at 150iterations 1.4450009E-03 2.9226303E-02 at 160iterations 8.0428837E-04 1.4846802E-02 at 170iterations 4.5337091E-04 1.1147499E-02 at 180iterations finished qdiffx linear iterations at : 14:06:38 total time elapsed so far: 19.42000 # loops : 180 mean,max change (kT/e) : 4.5337091E-04 1.1147499E-02 energy calculations done at 19.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.58000 DelPhi exited at 14:06:39 19.586u 0.456s 0:20.45 97.9% 0+0k 0+0io 0pf+0w