Sat Oct 8 23:19:59 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 Sat Oct 8 2011 at 23:19:59 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2260 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6550258 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): 83.68300 125.1770 ymin,ymax (A): 68.40400 120.4650 zmin,zma (A): 54.09800 108.4470 x,y,z range (A): 41.49400 52.06100 54.34900 scale (grids/A): 0.6550258 object centre (A): 104.4300 94.43449 81.27250 number of atom coordinates read : 2260 total number of charged atoms : 2126 net assigned charge : 10.51403 assigned positive charge : 332.1466 centred at (gu) : 91.46887 88.53806 89.30828 assigned negative charge : -321.6332 centred at (gu) : 91.36988 88.50558 89.30828 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6719 nv = 96 ne = 84 npr = 44827 no. pairs analyzed = 44827 no. exposed pairs = 2902 no. arc points = 20600 no. surface atoms = 982 nbur = 1278 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 3596 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2700000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1984 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6548591E-08 2.0078980E-08 midg,1,midg; midg,igrid,midg 2.4663164E-08 2.0629894E-08 1,midg,midg; igrid,midg,midg 6.6807981E-09 5.0420326E-08 gauss-seidel spectral radius is 0.9878978 estimated iterations to convergence 74 setup time was (sec) 0.4800000 now iterating at: 23:20:00 rms-change max change #iterations 0.1490730 21.06267 at 10iterations 1.5386489E-02 2.266899 at 20iterations 1.6676489E-03 0.2317429 at 30iterations 2.1881922E-04 3.2026291E-02 at 40iterations 4.2973519E-05 6.1016083E-03 at 50iterations finished qdiffx linear iterations at : 23:20:02 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 4.2973519E-05 6.1016083E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 23:20:02 3.074u 0.151s 0:03.50 92.0% 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 8 2011 at 23:20:03 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2260 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.965078 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): 83.68300 125.1770 ymin,ymax (A): 68.40400 120.4650 zmin,zma (A): 54.09800 108.4470 x,y,z range (A): 41.49400 52.06100 54.34900 scale (grids/A): 1.965078 object centre (A): 104.4300 94.43449 81.27250 number of atom coordinates read : 2260 total number of charged atoms : 2126 net assigned charge : 10.51403 assigned positive charge : 332.1466 centred at (gu) : 94.40633 85.61404 87.92444 assigned negative charge : -321.6332 centred at (gu) : 94.10989 85.51684 87.92486 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20600 grid for indexing accessible points = 1.400000 m= 26896 mr = 48960 m= 4640 mr = 19753 m= 336 mr = 2964 m= 3 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 990 time to turn everything in is 0.5200000 number of dielectric boundary points 31767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 16819 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) : 0.6550258 object centre at (A) : 104.4300 94.43449 81.27250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4980688E-02 3.8685609E-02 midg,1,midg; midg,igrid,midg 1.6488032E-02 4.1772325E-02 1,midg,midg; igrid,midg,midg -1.0857936E-03 3.6715314E-02 gauss-seidel spectral radius is 0.9986847 estimated iterations to convergence 218 setup time was (sec) 0.7700000 now iterating at: 23:20:03 rms-change max change #iterations 4.098869 190.2944 at 10iterations 1.953412 70.98407 at 20iterations 0.9215210 30.00024 at 30iterations 0.4367775 13.74850 at 40iterations 0.2077680 6.301167 at 50iterations 9.8487213E-02 3.133433 at 60iterations 4.6733432E-02 1.388987 at 70iterations 2.2193905E-02 0.6852207 at 80iterations 1.0580830E-02 0.3230953 at 90iterations 5.0350726E-03 0.1843624 at 100iterations 2.4040348E-03 8.1100464E-02 at 110iterations 1.1499265E-03 3.5919189E-02 at 120iterations finished qdiffx linear iterations at : 23:20:09 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 1.1499265E-03 3.5919189E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 23:20:10 6.894u 0.158s 0:07.42 94.8% 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 8 2011 at 23:20:10 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2260 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.947616 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): 83.68300 125.1770 ymin,ymax (A): 68.40400 120.4650 zmin,zma (A): 54.09800 108.4470 x,y,z range (A): 41.49400 52.06100 54.34900 scale (grids/A): 2.947616 object centre (A): 104.4300 94.43449 81.27250 number of atom coordinates read : 2260 total number of charged atoms : 2126 net assigned charge : 10.51403 assigned positive charge : 332.1466 centred at (gu) : 96.60959 83.42091 86.88680 assigned negative charge : -321.6332 centred at (gu) : 96.16486 83.27518 86.88722 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 165519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20600 grid for indexing accessible points = 1.400000 m= 85008 mr = 118581 m= 32432 mr = 69127 m= 8473 mr = 26092 m= 1547 mr = 6489 m= 122 mr = 1084 m= 4 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 3299 time to turn everything in is 1.240000 number of dielectric boundary points 71666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 17008 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) : 1.965078 object centre at (A) : 104.4300 94.43449 81.27250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4643686 0.3961027 midg,1,midg; midg,igrid,midg 0.1905778 0.5428928 1,midg,midg; igrid,midg,midg 7.1920489E-04 0.3280604 gauss-seidel spectral radius is 0.9992744 estimated iterations to convergence 293 setup time was (sec) 1.510000 now iterating at: 23:20:12 rms-change max change #iterations 9.630730 327.7100 at 10iterations 5.684965 158.2259 at 20iterations 3.346602 80.41049 at 30iterations 1.959655 45.92332 at 40iterations 1.144948 28.64741 at 50iterations 0.6659306 13.98190 at 60iterations 0.3876667 7.017595 at 70iterations 0.2255236 4.098167 at 80iterations 0.1307924 2.737118 at 90iterations 7.6040082E-02 1.486559 at 100iterations 4.4005897E-02 0.8280780 at 110iterations 2.5509620E-02 0.5430608 at 120iterations 1.4788639E-02 0.2963563 at 130iterations 8.5823098E-03 0.1620623 at 140iterations 4.9785874E-03 9.6019745E-02 at 150iterations 2.8987858E-03 5.7819366E-02 at 160iterations 1.6946419E-03 3.2066345E-02 at 170iterations 1.0053008E-03 2.0896912E-02 at 180iterations finished qdiffx linear iterations at : 23:20:21 total time elapsed so far: 10.94000 # loops : 180 mean,max change (kT/e) : 1.0053008E-03 2.0896912E-02 energy calculations done at 10.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.11000 DelPhi exited at 23:20:22 11.114u 0.198s 0:11.58 97.5% 0+0k 0+0io 0pf+0w