Sun Oct 9 20:44:23 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 20:44:23 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3885 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5371153 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): 32.54600 89.07500 ymin,ymax (A): -36.82100 15.31000 zmin,zma (A): 6.230999 72.51100 x,y,z range (A): 56.52900 52.13100 66.28000 scale (grids/A): 0.5371153 object centre (A): 60.81050 -10.75550 39.37100 number of atom coordinates read : 3885 total number of charged atoms : 3730 net assigned charge : 10.00001 assigned positive charge : 601.7303 centred at (gu) : 89.35680 89.05386 89.32687 assigned negative charge : -591.7329 centred at (gu) : 89.49383 89.12556 89.42288 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7153 nv = 96 ne = 84 npr = 77057 no. pairs analyzed = 77057 no. exposed pairs = 5134 no. arc points = 35489 no. surface atoms = 1707 nbur = 2178 mkacc time = 0.1300000 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= 323 mr = 3543 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3547 ## 440 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9460 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2091682E-09 -1.5790361E-10 midg,1,midg; midg,igrid,midg 1.1041132E-09 -2.3004813E-11 1,midg,midg; igrid,midg,midg 1.4962921E-09 -3.8552325E-10 gauss-seidel spectral radius is 0.9822035 estimated iterations to convergence 62 setup time was (sec) 0.4500000 now iterating at: 20:44:23 rms-change max change #iterations 7.8010879E-02 12.83093 at 10iterations 5.6577274E-03 0.8081741 at 20iterations 1.1817381E-03 0.1397266 at 30iterations 4.6420700E-04 5.8680058E-02 at 40iterations 1.9850268E-04 2.7292252E-02 at 50iterations finished qdiffx linear iterations at : 20:44:26 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.9850268E-04 2.7292252E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 20:44:27 3.471u 0.192s 0:04.01 91.2% 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 20:44:27 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3885 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.611346 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): 32.54600 89.07500 ymin,ymax (A): -36.82100 15.31000 zmin,zma (A): 6.230999 72.51100 x,y,z range (A): 56.52900 52.13100 66.28000 scale (grids/A): 1.611346 object centre (A): 60.81050 -10.75550 39.37100 number of atom coordinates read : 3885 total number of charged atoms : 3730 net assigned charge : 10.00001 assigned positive charge : 601.7303 centred at (gu) : 88.06952 87.16069 87.97968 assigned negative charge : -591.7329 centred at (gu) : 88.48127 87.37667 88.26806 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 78361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35489 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25721 mr = 52063 m= 2888 mr = 17353 m= 90 mr = 1463 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 36177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 28373 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) : 0.5371153 object centre at (A) : 60.81050 -10.75550 39.37100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4325147E-02 -2.8324546E-03 midg,1,midg; midg,igrid,midg 2.9870547E-02 9.8075420E-03 1,midg,midg; igrid,midg,midg 8.5500972E-03 -3.2113970E-03 gauss-seidel spectral radius is 0.9982328 estimated iterations to convergence 189 setup time was (sec) 0.6100000 now iterating at: 20:44:28 rms-change max change #iterations 3.831966 146.1918 at 10iterations 1.617343 58.06858 at 20iterations 0.6803682 24.27094 at 30iterations 0.2871534 8.970071 at 40iterations 0.1213575 4.363350 at 50iterations 5.1093854E-02 1.718807 at 60iterations 2.1724714E-02 0.7306747 at 70iterations 9.3369149E-03 0.3094063 at 80iterations 4.1760653E-03 0.1581810 at 90iterations 2.0044656E-03 6.5934181E-02 at 100iterations 1.1097207E-03 3.6413670E-02 at 110iterations 7.1898522E-04 2.3056030E-02 at 120iterations finished qdiffx linear iterations at : 20:44:35 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 7.1898522E-04 2.3056030E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 20:44:35 7.874u 0.217s 0:08.36 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 Sun Oct 9 2011 at 20:44:35 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3885 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.417019 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): 32.54600 89.07500 ymin,ymax (A): -36.82100 15.31000 zmin,zma (A): 6.230999 72.51100 x,y,z range (A): 56.52900 52.13100 66.28000 scale (grids/A): 2.417019 object centre (A): 60.81050 -10.75550 39.37100 number of atom coordinates read : 3885 total number of charged atoms : 3730 net assigned charge : 10.00001 assigned positive charge : 601.7303 centred at (gu) : 87.10393 85.74066 86.96928 assigned negative charge : -591.7329 centred at (gu) : 87.72160 86.06508 87.40198 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 181836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35489 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 86214 mr = 127936 m= 26400 mr = 67113 m= 4651 mr = 19720 m= 343 mr = 3043 m= 4 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 81486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 29793 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) : 1.611346 object centre at (A) : 60.81050 -10.75550 39.37100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2279010 9.8307999E-03 midg,1,midg; midg,igrid,midg 0.4885783 0.1779260 1,midg,midg; igrid,midg,midg 2.9610936E-02 -1.6170129E-02 gauss-seidel spectral radius is 0.9991835 estimated iterations to convergence 276 setup time was (sec) 1.200000 now iterating at: 20:44:37 rms-change max change #iterations 10.20246 324.9435 at 10iterations 5.949748 163.1583 at 20iterations 3.434223 86.41373 at 30iterations 1.974775 41.80072 at 40iterations 1.126115 25.48690 at 50iterations 0.6406059 13.67419 at 60iterations 0.3631662 7.773148 at 70iterations 0.2052496 4.310421 at 80iterations 0.1158535 2.674667 at 90iterations 6.5391995E-02 1.318355 at 100iterations 3.6804814E-02 0.7064652 at 110iterations 2.0793578E-02 0.4234638 at 120iterations 1.1708757E-02 0.2534370 at 130iterations 6.6535692E-03 0.1319904 at 140iterations 3.8121971E-03 7.2719574E-02 at 150iterations 2.2393779E-03 4.8875012E-02 at 160iterations 1.3701909E-03 3.4275055E-02 at 170iterations 8.9339301E-04 2.0352364E-02 at 180iterations finished qdiffx linear iterations at : 20:44:48 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 8.9339301E-04 2.0352364E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 20:44:48 12.829u 0.215s 0:13.32 97.8% 0+0k 0+0io 0pf+0w