Thu Jan 19 13:34:06 PST 2012 #!/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 Thu Jan 19 2012 at 13:34:07 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: 378 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6770 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4308832 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): -4.598000 78.02300 ymin,ymax (A): -1.041000 74.31700 zmin,zma (A): 167.0470 236.5830 x,y,z range (A): 82.62100 75.35800 69.53600 scale (grids/A): 0.4308832 object centre (A): 36.71250 36.63800 201.8150 number of atom coordinates read : 6770 total number of charged atoms : 6607 net assigned charge : 3.200027 assigned positive charge : 1030.406 centred at (gu) : 88.65636 90.32172 89.58438 assigned negative charge : -1027.215 centred at (gu) : 88.66104 90.36494 89.56281 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7365 nv = 96 ne = 84 npr = 136227 no. pairs analyzed = 136227 no. exposed pairs = 8917 no. arc points = 60247 no. surface atoms = 3006 nbur = 3764 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 = 1.932000 m= 210 mr = 3428 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5015 ## 1050 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.3708447E-13 1.8503070E-12 midg,1,midg; midg,igrid,midg 3.1780652E-12 -2.4015828E-12 1,midg,midg; igrid,midg,midg 1.5087231E-12 2.5911684E-13 gauss-seidel spectral radius is 0.9726666 estimated iterations to convergence 50 setup time was (sec) 0.6200000 now iterating at: 13:34:10 rms-change max change #iterations 3.1446714E-02 5.614042 at 10iterations 1.9644108E-03 0.3661060 at 20iterations 7.2010915E-04 0.1398964 at 30iterations 3.0927258E-04 6.0014725E-02 at 40iterations 1.3275963E-04 2.5553703E-02 at 50iterations finished qdiffx linear iterations at : 13:34:19 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 1.3275963E-04 2.5553703E-02 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 13:34:20 3.821u 0.180s 0:13.13 30.4% 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 Thu Jan 19 2012 at 13:34:21 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: 378 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6770 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.292650 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): -4.598000 78.02300 ymin,ymax (A): -1.041000 74.31700 zmin,zma (A): 167.0470 236.5830 x,y,z range (A): 82.62100 75.35800 69.53600 scale (grids/A): 1.292650 object centre (A): 36.71250 36.63800 201.8150 number of atom coordinates read : 6770 total number of charged atoms : 6607 net assigned charge : 3.200027 assigned positive charge : 1030.406 centred at (gu) : 85.96704 90.96312 88.75125 assigned negative charge : -1027.215 centred at (gu) : 85.98249 91.09440 88.68833 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 85764 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60247 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 19995 mr = 55819 m= 1015 mr = 11770 m= 12 mr = 214 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 601 time to turn everything in is 0.4700000 number of dielectric boundary points 38983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1095 ## 34 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 45805 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) : 0.4308832 object centre at (A) : 36.71250 36.63800 201.8150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4663759E-04 6.3954758E-05 midg,1,midg; midg,igrid,midg 2.6339418E-03 6.9763092E-04 1,midg,midg; igrid,midg,midg 2.1647755E-03 3.0575821E-03 gauss-seidel spectral radius is 0.9974150 estimated iterations to convergence 157 setup time was (sec) 0.7000000 now iterating at: 13:34:23 rms-change max change #iterations 3.084519 134.2200 at 10iterations 1.089033 43.36552 at 20iterations 0.3835318 12.85439 at 30iterations 0.1354768 5.490690 at 40iterations 4.8033625E-02 1.590987 at 50iterations 1.7095694E-02 0.6102009 at 60iterations 6.3130897E-03 0.2295513 at 70iterations 2.6010287E-03 0.1185646 at 80iterations 1.3414217E-03 5.6612968E-02 at 90iterations 8.6090626E-04 3.5910606E-02 at 100iterations 6.0993852E-04 2.4374008E-02 at 110iterations 4.4433316E-04 1.7580032E-02 at 120iterations finished qdiffx linear iterations at : 13:34:40 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 4.4433316E-04 1.7580032E-02 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 13:34:41 8.437u 0.242s 0:20.47 42.3% 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 Thu Jan 19 2012 at 13:34:42 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: 378 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6770 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.938974 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): -4.598000 78.02300 ymin,ymax (A): -1.041000 74.31700 zmin,zma (A): 167.0470 236.5830 x,y,z range (A): 82.62100 75.35800 69.53600 scale (grids/A): 1.938974 object centre (A): 36.71250 36.63800 201.8150 number of atom coordinates read : 6770 total number of charged atoms : 6607 net assigned charge : 3.200027 assigned positive charge : 1030.406 centred at (gu) : 83.95016 91.44427 88.12640 assigned negative charge : -1027.215 centred at (gu) : 83.97381 91.64166 88.03213 start vw surface at 0.1700000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 201453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60247 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 77415 mr = 140194 m= 13971 mr = 56509 m= 998 mr = 8735 m= 23 mr = 383 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 2035 time to turn everything in is 1.050000 number of dielectric boundary points 88039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 347 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 52168 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) : 1.292650 object centre at (A) : 36.71250 36.63800 201.8150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9004876E-02 -6.1190589E-03 midg,1,midg; midg,igrid,midg 4.4753909E-02 6.7772910E-02 1,midg,midg; igrid,midg,midg 0.1832309 0.1590813 gauss-seidel spectral radius is 0.9989850 estimated iterations to convergence 248 setup time was (sec) 1.310000 now iterating at: 13:34:47 rms-change max change #iterations 9.490939 250.2864 at 10iterations 5.162143 132.3322 at 20iterations 2.781024 69.46584 at 30iterations 1.488716 38.21105 at 40iterations 0.7912047 18.93593 at 50iterations 0.4203081 9.995134 at 60iterations 0.2220814 5.409299 at 70iterations 0.1171251 2.733191 at 80iterations 6.1789084E-02 1.290222 at 90iterations 3.2562740E-02 0.6723633 at 100iterations 1.7112639E-02 0.3681567 at 110iterations 8.9745298E-03 0.2006168 at 120iterations 4.7296756E-03 9.7444534E-02 at 130iterations 2.4846336E-03 5.6880713E-02 at 140iterations 1.3170055E-03 2.6366234E-02 at 150iterations 7.0507044E-04 1.4624596E-02 at 160iterations 3.8809795E-04 8.3751678E-03 at 170iterations 2.2355007E-04 5.6476593E-03 at 180iterations finished qdiffx linear iterations at : 13:35:22 total time elapsed so far: 13.18000 # loops : 180 mean,max change (kT/e) : 2.2355007E-04 5.6476593E-03 energy calculations done at 13.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 13:35:23 13.314u 0.219s 0:40.84 33.1% 0+0k 0+0io 0pf+0w