Tue Oct 11 03:18:57 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 Tue Oct 11 2011 at 03:18:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 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: 0.5376425 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): -42.98900 10.77800 ymin,ymax (A): -55.92000 3.374000 zmin,zma (A): -34.45400 31.76100 x,y,z range (A): 53.76700 59.29400 66.21500 scale (grids/A): 0.5376425 object centre (A): -16.10550 -26.27300 -1.346501 number of atom coordinates read : 3415 total number of charged atoms : 3274 net assigned charge : -5.999976 assigned positive charge : 516.9323 centred at (gu) : 91.43718 87.91486 92.25008 assigned negative charge : -522.9338 centred at (gu) : 91.40717 87.88343 92.25662 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6422 nv = 96 ne = 84 npr = 69194 no. pairs analyzed = 69194 no. exposed pairs = 4286 no. arc points = 30340 no. surface atoms = 1434 nbur = 1981 mkacc time = 0.1800000 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 = 1.596000 m= 260 mr = 3328 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3148 ## 469 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8494 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3176553E-10 -5.2201976E-10 midg,1,midg; midg,igrid,midg -7.4137418E-10 -5.4832004E-11 1,midg,midg; igrid,midg,midg -3.0260638E-10 -1.3000429E-10 gauss-seidel spectral radius is 0.9822024 estimated iterations to convergence 62 setup time was (sec) 0.7100000 now iterating at: 03:18:58 rms-change max change #iterations 7.4789226E-02 13.80099 at 10iterations 5.0704703E-03 0.7852726 at 20iterations 5.9730135E-04 8.3329439E-02 at 30iterations 1.4100925E-04 1.7755985E-02 at 40iterations 3.8279850E-05 4.8402548E-03 at 50iterations finished qdiffx linear iterations at : 03:19:03 total time elapsed so far: 5.410000 # loops : 50 mean,max change (kT/e) : 3.8279850E-05 4.8402548E-03 energy calculations done at 5.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.580000 DelPhi exited at 03:19:03 5.586u 0.418s 0:06.33 94.6% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 03:19:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 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: 1.612927 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): -42.98900 10.77800 ymin,ymax (A): -55.92000 3.374000 zmin,zma (A): -34.45400 31.76100 x,y,z range (A): 53.76700 59.29400 66.21500 scale (grids/A): 1.612927 object centre (A): -16.10550 -26.27300 -1.346501 number of atom coordinates read : 3415 total number of charged atoms : 3274 net assigned charge : -5.999976 assigned positive charge : 516.9323 centred at (gu) : 94.31065 83.74372 96.74928 assigned negative charge : -522.9338 centred at (gu) : 94.22105 83.64977 96.76965 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30340 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21841 mr = 48506 m= 2247 mr = 14803 m= 65 mr = 1026 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 394 time to turn everything in is 0.6400000 number of dielectric boundary points 31149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 405 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 24959 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) : 0.5376425 object centre at (A) : -16.10550 -26.27300 -1.346501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4460964E-02 -1.4520777E-02 midg,1,midg; midg,igrid,midg -5.8021424E-03 -9.7459531E-04 1,midg,midg; igrid,midg,midg -5.9623569E-03 -2.6525264E-03 gauss-seidel spectral radius is 0.9981767 estimated iterations to convergence 186 setup time was (sec) 1.000000 now iterating at: 03:19:05 rms-change max change #iterations 3.535296 181.0160 at 10iterations 1.462405 54.54596 at 20iterations 0.6096626 26.23785 at 30iterations 0.2538309 8.833418 at 40iterations 0.1059365 4.070879 at 50iterations 4.3966986E-02 1.555166 at 60iterations 1.8375846E-02 0.6909199 at 70iterations 7.7538523E-03 0.2749257 at 80iterations 3.3184523E-03 0.1198273 at 90iterations 1.4662944E-03 4.9336910E-02 at 100iterations 6.8288838E-04 2.4425745E-02 at 110iterations 3.4882914E-04 1.1816554E-02 at 120iterations finished qdiffx linear iterations at : 03:19:17 total time elapsed so far: 13.62000 # loops : 120 mean,max change (kT/e) : 3.4882914E-04 1.1816554E-02 energy calculations done at 13.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 03:19:18 13.801u 0.474s 0:14.76 96.6% 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 Tue Oct 11 2011 at 03:19:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 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: 2.419391 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): -42.98900 10.77800 ymin,ymax (A): -55.92000 3.374000 zmin,zma (A): -34.45400 31.76100 x,y,z range (A): 53.76700 59.29400 66.21500 scale (grids/A): 2.419391 object centre (A): -16.10550 -26.27300 -1.346501 number of atom coordinates read : 3415 total number of charged atoms : 3274 net assigned charge : -5.999976 assigned positive charge : 516.9323 centred at (gu) : 96.46576 80.61526 100.1237 assigned negative charge : -522.9338 centred at (gu) : 96.33144 80.47459 100.1543 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 166027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30340 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 76309 mr = 119093 m= 21119 mr = 59912 m= 3467 mr = 15588 m= 224 mr = 2174 m= 3 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1295 time to turn everything in is 1.520000 number of dielectric boundary points 70303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 26155 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) : 1.612927 object centre at (A) : -16.10550 -26.27300 -1.346501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4444822 -0.3674446 midg,1,midg; midg,igrid,midg -3.3928059E-02 3.3129156E-02 1,midg,midg; igrid,midg,midg -9.8269001E-02 -3.4392178E-02 gauss-seidel spectral radius is 0.9991438 estimated iterations to convergence 270 setup time was (sec) 1.900000 now iterating at: 03:19:21 rms-change max change #iterations 9.236073 309.8139 at 10iterations 5.225261 132.7826 at 20iterations 2.934469 63.52640 at 30iterations 1.639329 35.38230 at 40iterations 0.9123626 19.67956 at 50iterations 0.5082163 11.02023 at 60iterations 0.2818063 5.891109 at 70iterations 0.1559865 3.382451 at 80iterations 8.6513519E-02 1.921576 at 90iterations 4.7826070E-02 1.005280 at 100iterations 2.6367076E-02 0.5127888 at 110iterations 1.4606841E-02 0.2928123 at 120iterations 8.0820760E-03 0.1653404 at 130iterations 4.4905753E-03 9.1185331E-02 at 140iterations 2.4982446E-03 4.7888279E-02 at 150iterations 1.4011672E-03 2.9253960E-02 at 160iterations 7.9510140E-04 1.5548706E-02 at 170iterations 4.6174286E-04 1.0166645E-02 at 180iterations finished qdiffx linear iterations at : 03:19:41 total time elapsed so far: 22.41000 # loops : 180 mean,max change (kT/e) : 4.6174286E-04 1.0166645E-02 energy calculations done at 22.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.58000 DelPhi exited at 03:19:42 22.586u 0.515s 0:23.41 98.6% 0+0k 0+0io 0pf+0w