Sat Oct 15 11:25:58 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 Sat Oct 15 2011 at 11:25:59 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 = 3259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5582825 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): -14.07400 42.38000 ymin,ymax (A): -38.48600 25.28100 zmin,zma (A): -15.66400 34.00700 x,y,z range (A): 56.45400 63.76700 49.67100 scale (grids/A): 0.5582825 object centre (A): 14.15300 -6.602500 9.171500 number of atom coordinates read : 3259 total number of charged atoms : 3115 net assigned charge : -1.999989 assigned positive charge : 485.4318 centred at (gu) : 91.01770 91.79140 90.29544 assigned negative charge : -487.4330 centred at (gu) : 90.99091 91.76824 90.26062 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6547 nv = 96 ne = 84 npr = 67605 no. pairs analyzed = 67605 no. exposed pairs = 3886 no. arc points = 27479 no. surface atoms = 1313 nbur = 1946 mkacc time = 0.1200000 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 = 1.540000 m= 267 mr = 3597 m= 0 mr = 13 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2726 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8478 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6436916E-10 2.0055778E-10 midg,1,midg; midg,igrid,midg -3.0794459E-10 9.1193594E-11 1,midg,midg; igrid,midg,midg -4.0249934E-10 1.2546901E-10 gauss-seidel spectral radius is 0.9834661 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 11:25:59 rms-change max change #iterations 8.4925331E-02 15.15045 at 10iterations 6.1024725E-03 0.9746933 at 20iterations 5.2493892E-04 8.3030701E-02 at 30iterations 7.8356534E-05 1.1014462E-02 at 40iterations 1.7979795E-05 2.5904179E-03 at 50iterations finished qdiffx linear iterations at : 11:26:02 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 1.7979795E-05 2.5904179E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 11:26:03 3.669u 0.217s 0:04.32 89.5% 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 Sat Oct 15 2011 at 11:26:03 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 = 3259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.674847 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): -14.07400 42.38000 ymin,ymax (A): -38.48600 25.28100 zmin,zma (A): -15.66400 34.00700 x,y,z range (A): 56.45400 63.76700 49.67100 scale (grids/A): 1.674847 object centre (A): 14.15300 -6.602500 9.171500 number of atom coordinates read : 3259 total number of charged atoms : 3115 net assigned charge : -1.999989 assigned positive charge : 485.4318 centred at (gu) : 93.05234 95.37315 90.88561 assigned negative charge : -487.4330 centred at (gu) : 92.97238 95.30449 90.78139 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72252 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27479 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23378 mr = 50610 m= 2496 mr = 16668 m= 79 mr = 1194 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 930 time to turn everything in is 0.3700000 number of dielectric boundary points 29730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 298 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 24008 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) : 0.5582825 object centre at (A) : 14.15300 -6.602500 9.171500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7305672E-03 4.4171154E-03 midg,1,midg; midg,igrid,midg 5.1840222E-03 7.7746459E-04 1,midg,midg; igrid,midg,midg -4.5631407E-03 -1.2747229E-03 gauss-seidel spectral radius is 0.9982935 estimated iterations to convergence 192 setup time was (sec) 0.6100000 now iterating at: 11:26:04 rms-change max change #iterations 3.667517 168.1593 at 10iterations 1.564225 57.53707 at 20iterations 0.6730345 25.11787 at 30iterations 0.2880444 9.577248 at 40iterations 0.1236419 4.808350 at 50iterations 5.2904777E-02 1.822662 at 60iterations 2.2759298E-02 0.8581140 at 70iterations 9.7746514E-03 0.3526981 at 80iterations 4.1952031E-03 0.1481237 at 90iterations 1.8117164E-03 6.8171024E-02 at 100iterations 7.8274682E-04 2.6458740E-02 at 110iterations 3.4187798E-04 1.1753082E-02 at 120iterations finished qdiffx linear iterations at : 11:26:11 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 3.4187798E-04 1.1753082E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 11:26:12 8.379u 0.256s 0:09.41 91.6% 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 Sat Oct 15 2011 at 11:26:12 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 = 3259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.512271 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): -14.07400 42.38000 ymin,ymax (A): -38.48600 25.28100 zmin,zma (A): -15.66400 34.00700 x,y,z range (A): 56.45400 63.76700 49.67100 scale (grids/A): 2.512271 object centre (A): 14.15300 -6.602500 9.171500 number of atom coordinates read : 3259 total number of charged atoms : 3115 net assigned charge : -1.999989 assigned positive charge : 485.4318 centred at (gu) : 94.57819 98.05946 91.32811 assigned negative charge : -487.4330 centred at (gu) : 94.45844 97.95646 91.17207 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 167885 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27479 grid for indexing accessible points = 1.400000 m= 80270 mr = 123206 m= 23630 mr = 65053 m= 3953 mr = 18101 m= 314 mr = 2526 m= 6 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 3102 time to turn everything in is 0.9100000 number of dielectric boundary points 67061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 24902 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) : 1.674847 object centre at (A) : 14.15300 -6.602500 9.171500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1518735 8.3564326E-02 midg,1,midg; midg,igrid,midg 5.6450531E-02 -1.6802792E-02 1,midg,midg; igrid,midg,midg -1.7593510E-02 2.7185332E-03 gauss-seidel spectral radius is 0.9991726 estimated iterations to convergence 275 setup time was (sec) 1.150000 now iterating at: 11:26:14 rms-change max change #iterations 9.281625 336.7090 at 10iterations 5.234967 131.7365 at 20iterations 2.948309 59.50554 at 30iterations 1.654573 32.16322 at 40iterations 0.9275033 19.13224 at 50iterations 0.5179786 9.808296 at 60iterations 0.2890694 6.668857 at 70iterations 0.1611619 3.164627 at 80iterations 9.0123005E-02 1.740225 at 90iterations 5.0080214E-02 1.046670 at 100iterations 2.7946774E-02 0.5244827 at 110iterations 1.5586441E-02 0.3111305 at 120iterations 8.6888373E-03 0.1697006 at 130iterations 4.8389169E-03 8.7985992E-02 at 140iterations 2.6997270E-03 5.1522255E-02 at 150iterations 1.5118393E-03 2.8922081E-02 at 160iterations 8.5040356E-04 1.7053485E-02 at 170iterations 4.7985377E-04 9.4246864E-03 at 180iterations finished qdiffx linear iterations at : 11:26:26 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 4.7985377E-04 9.4246864E-03 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.90000 DelPhi exited at 11:26:27 13.905u 0.259s 0:14.69 96.3% 0+0k 0+0io 0pf+0w