Sun Oct 9 01:48:50 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 01:48:50 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2297 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6519191 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): -27.55700 26.46900 ymin,ymax (A): 8.278000 50.50400 zmin,zma (A): -11.58900 43.01900 x,y,z range (A): 54.02600 42.22600 54.60800 scale (grids/A): 0.6519191 object centre (A): -0.5439997 29.39100 15.71500 number of atom coordinates read : 2297 total number of charged atoms : 2163 net assigned charge : 11.01402 assigned positive charge : 337.9645 centred at (gu) : 91.11710 91.47058 91.02108 assigned negative charge : -326.9511 centred at (gu) : 91.14152 91.43946 91.01902 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6746 nv = 96 ne = 84 npr = 45767 no. pairs analyzed = 45767 no. exposed pairs = 3034 no. arc points = 21632 no. surface atoms = 1024 nbur = 1273 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 3512 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.1700000 number of dielectric boundary points 3596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2129 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7877 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7934438E-08 2.7823274E-08 midg,1,midg; midg,igrid,midg 1.3524604E-08 3.5881801E-08 1,midg,midg; igrid,midg,midg 2.0394296E-08 2.3830660E-08 gauss-seidel spectral radius is 0.9877888 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 01:48:51 rms-change max change #iterations 0.1478489 22.44943 at 10iterations 1.5126454E-02 2.413421 at 20iterations 1.5619565E-03 0.2113075 at 30iterations 1.6120716E-04 2.8366089E-02 at 40iterations 1.8191176E-05 2.5482178E-03 at 50iterations finished qdiffx linear iterations at : 01:48:54 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.8191176E-05 2.5482178E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 01:48:54 3.411u 0.189s 0:04.01 89.5% 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 Sun Oct 9 2011 at 01:48:54 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2297 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.955757 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): -27.55700 26.46900 ymin,ymax (A): 8.278000 50.50400 zmin,zma (A): -11.58900 43.01900 x,y,z range (A): 54.02600 42.22600 54.60800 scale (grids/A): 1.955757 object centre (A): -0.5439997 29.39100 15.71500 number of atom coordinates read : 2297 total number of charged atoms : 2163 net assigned charge : 11.01402 assigned positive charge : 337.9645 centred at (gu) : 93.35088 94.41155 93.06293 assigned negative charge : -326.9511 centred at (gu) : 93.42458 94.31866 93.05723 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72085 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21632 grid for indexing accessible points = 1.400000 m= 25440 mr = 48116 m= 4101 mr = 18171 m= 263 mr = 2452 m= 2 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 33050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17089 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) : 0.6519191 object centre at (A) : -0.5439997 29.39100 15.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3602669E-02 4.3887965E-02 midg,1,midg; midg,igrid,midg -9.0967154E-04 2.9720578E-02 1,midg,midg; igrid,midg,midg 5.2250765E-02 6.0749479E-02 gauss-seidel spectral radius is 0.9986790 estimated iterations to convergence 218 setup time was (sec) 0.5800000 now iterating at: 01:48:55 rms-change max change #iterations 4.092823 210.6979 at 10iterations 1.936430 67.06364 at 20iterations 0.9152226 29.81083 at 30iterations 0.4328121 13.78891 at 40iterations 0.2049510 7.769295 at 50iterations 9.6575506E-02 3.054438 at 60iterations 4.5800310E-02 1.574884 at 70iterations 2.1707140E-02 0.7392769 at 80iterations 1.0299277E-02 0.3566685 at 90iterations 4.8753037E-03 0.1555185 at 100iterations 2.3134092E-03 7.7131391E-02 at 110iterations 1.1008409E-03 3.4764767E-02 at 120iterations finished qdiffx linear iterations at : 01:49:02 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.1008409E-03 3.4764767E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 01:49:03 7.945u 0.211s 0:08.47 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 Sun Oct 9 2011 at 01:49:03 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2297 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.933636 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): -27.55700 26.46900 ymin,ymax (A): 8.278000 50.50400 zmin,zma (A): -11.58900 43.01900 x,y,z range (A): 54.02600 42.22600 54.60800 scale (grids/A): 2.933636 object centre (A): -0.5439997 29.39100 15.71500 number of atom coordinates read : 2297 total number of charged atoms : 2163 net assigned charge : 11.01402 assigned positive charge : 337.9645 centred at (gu) : 95.02626 96.61713 94.59439 assigned negative charge : -326.9511 centred at (gu) : 95.13684 96.47794 94.58578 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166182 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21632 grid for indexing accessible points = 1.400000 m= 81620 mr = 116932 m= 29970 mr = 65410 m= 7382 mr = 23598 m= 1148 mr = 5388 m= 82 mr = 727 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 74291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 17304 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) : 1.955757 object centre at (A) : -0.5439997 29.39100 15.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7258765 0.4625854 midg,1,midg; midg,igrid,midg -2.3536963E-02 0.2893907 1,midg,midg; igrid,midg,midg 0.5359935 0.5226145 gauss-seidel spectral radius is 0.9992785 estimated iterations to convergence 294 setup time was (sec) 1.170000 now iterating at: 01:49:04 rms-change max change #iterations 9.736688 394.9734 at 10iterations 5.765781 159.1696 at 20iterations 3.391592 71.01355 at 30iterations 1.989474 42.19035 at 40iterations 1.161465 22.49530 at 50iterations 0.6776710 15.15646 at 60iterations 0.3946781 7.772642 at 70iterations 0.2286685 4.795948 at 80iterations 0.1329821 2.678713 at 90iterations 7.7092819E-02 1.492167 at 100iterations 4.4695430E-02 0.8413677 at 110iterations 2.5965625E-02 0.5733027 at 120iterations 1.4981685E-02 0.2671318 at 130iterations 8.7158047E-03 0.1699142 at 140iterations 5.0328351E-03 9.7945690E-02 at 150iterations 2.9213182E-03 5.5856228E-02 at 160iterations 1.6967237E-03 3.2485962E-02 at 170iterations 9.8309177E-04 2.0401001E-02 at 180iterations finished qdiffx linear iterations at : 01:49:16 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 9.8309177E-04 2.0401001E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 01:49:16 12.890u 0.219s 0:13.60 96.3% 0+0k 0+0io 0pf+0w