Sat Oct 8 18:39:30 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 18:39:30 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6254832 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): -32.07100 17.49100 ymin,ymax (A): -23.21800 23.30900 zmin,zma (A): -12.45100 44.46500 x,y,z range (A): 49.56200 46.52700 56.91600 scale (grids/A): 0.6254832 object centre (A): -7.290000 4.5499802E-02 16.00700 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 392.6040 centred at (gu) : 88.57900 89.01723 89.91697 assigned negative charge : -388.1046 centred at (gu) : 88.48886 89.08050 89.77901 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6622 nv = 96 ne = 84 npr = 54141 no. pairs analyzed = 54141 no. exposed pairs = 2942 no. arc points = 20737 no. surface atoms = 1007 nbur = 1586 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 343 mr = 3778 m= 0 mr = 48 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3000000 number of dielectric boundary points 3139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2084 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8109 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6515105E-09 1.4617807E-08 midg,1,midg; midg,igrid,midg 1.1429540E-08 -4.4140708E-10 1,midg,midg; igrid,midg,midg -3.8439456E-09 8.2859799E-09 gauss-seidel spectral radius is 0.9867552 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 18:39:31 rms-change max change #iterations 0.1351734 20.57433 at 10iterations 1.2873615E-02 1.812872 at 20iterations 1.2204440E-03 0.1906548 at 30iterations 1.1316270E-04 1.5399933E-02 at 40iterations 1.0749924E-05 1.3313293E-03 at 50iterations finished qdiffx linear iterations at : 18:39:34 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.0749924E-05 1.3313293E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 18:39:34 3.357u 0.227s 0:03.88 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 18:39:34 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.876449 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): -32.07100 17.49100 ymin,ymax (A): -23.21800 23.30900 zmin,zma (A): -12.45100 44.46500 x,y,z range (A): 49.56200 46.52700 56.91600 scale (grids/A): 1.876449 object centre (A): -7.290000 4.5499802E-02 16.00700 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 392.6040 centred at (gu) : 85.73673 87.05135 89.75037 assigned negative charge : -388.1046 centred at (gu) : 85.46648 87.24139 89.33673 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20737 grid for indexing accessible points = 1.400000 m= 26198 mr = 51264 m= 3862 mr = 19895 m= 235 mr = 2463 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3549 time to turn everything in is 0.5300000 number of dielectric boundary points 28911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19242 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) : 0.6254832 object centre at (A) : -7.290000 4.5499802E-02 16.00700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7328001E-02 3.3163439E-02 midg,1,midg; midg,igrid,midg 1.8486248E-02 3.8463587E-03 1,midg,midg; igrid,midg,midg -4.6332963E-03 3.4384735E-02 gauss-seidel spectral radius is 0.9985871 estimated iterations to convergence 211 setup time was (sec) 0.8300000 now iterating at: 18:39:35 rms-change max change #iterations 4.085656 187.5133 at 10iterations 1.894437 62.89953 at 20iterations 0.8764548 27.86453 at 30iterations 0.4035348 13.72098 at 40iterations 0.1875779 5.900244 at 50iterations 8.6799622E-02 2.718948 at 60iterations 4.0081982E-02 1.237282 at 70iterations 1.8585006E-02 0.5910408 at 80iterations 8.5900910E-03 0.2889099 at 90iterations 3.9636465E-03 0.1310673 at 100iterations 1.8416422E-03 5.6198120E-02 at 110iterations 8.5003127E-04 2.7572632E-02 at 120iterations finished qdiffx linear iterations at : 18:39:42 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 8.5003127E-04 2.7572632E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 18:39:42 7.461u 0.230s 0:07.96 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 Sat Oct 8 2011 at 18:39:42 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.814674 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): -32.07100 17.49100 ymin,ymax (A): -23.21800 23.30900 zmin,zma (A): -12.45100 44.46500 x,y,z range (A): 49.56200 46.52700 56.91600 scale (grids/A): 2.814674 object centre (A): -7.290000 4.5499802E-02 16.00700 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 392.6040 centred at (gu) : 83.60494 85.57687 89.62552 assigned negative charge : -388.1046 centred at (gu) : 83.19966 85.86191 89.00513 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 167398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20737 grid for indexing accessible points = 1.400000 m= 85888 mr = 123821 m= 30281 mr = 71771 m= 6944 mr = 24698 m= 997 mr = 5335 m= 58 mr = 670 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 11880 time to turn everything in is 1.300000 number of dielectric boundary points 65245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 19622 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) : 1.876449 object centre at (A) : -7.290000 4.5499802E-02 16.00700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2030151 0.3954682 midg,1,midg; midg,igrid,midg 0.2021332 6.0607299E-02 1,midg,midg; igrid,midg,midg -2.1893193E-03 0.4387811 gauss-seidel spectral radius is 0.9992378 estimated iterations to convergence 286 setup time was (sec) 1.610000 now iterating at: 18:39:44 rms-change max change #iterations 9.551423 326.2109 at 10iterations 5.476665 124.1045 at 20iterations 3.131458 58.27145 at 30iterations 1.785900 39.18817 at 40iterations 1.017059 17.87390 at 50iterations 0.5791852 10.12045 at 60iterations 0.3307399 5.814568 at 70iterations 0.1881731 3.957186 at 80iterations 0.1069089 1.946586 at 90iterations 6.0809612E-02 1.125981 at 100iterations 3.4621824E-02 0.6292019 at 110iterations 1.9742649E-02 0.4319044 at 120iterations 1.1212607E-02 0.2110004 at 130iterations 6.3974457E-03 0.1209087 at 140iterations 3.6401055E-03 7.0425034E-02 at 150iterations 2.0727164E-03 3.7994385E-02 at 160iterations 1.1812283E-03 2.4369240E-02 at 170iterations 6.6953024E-04 1.2290955E-02 at 180iterations finished qdiffx linear iterations at : 18:39:54 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 6.6953024E-04 1.2290955E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 18:39:55 12.215u 0.250s 0:12.75 97.7% 0+0k 0+0io 0pf+0w