Sun Oct 9 04:47:27 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 04:47:27 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2716 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: 0.6149382 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): -10.63100 35.20500 ymin,ymax (A): 4.6000004E-02 57.93800 zmin,zma (A): -25.19700 27.23700 x,y,z range (A): 45.83600 57.89200 52.43400 scale (grids/A): 0.6149382 object centre (A): 12.28700 28.99200 1.020000 number of atom coordinates read : 2716 total number of charged atoms : 2578 net assigned charge : 6.500036 assigned positive charge : 405.3073 centred at (gu) : 90.08564 88.79105 89.67654 assigned negative charge : -398.8084 centred at (gu) : 90.17717 88.68330 89.65983 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6895 nv = 96 ne = 84 npr = 53910 no. pairs analyzed = 53910 no. exposed pairs = 3732 no. arc points = 25862 no. surface atoms = 1255 nbur = 1461 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3452 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2580 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8469 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8424699E-09 5.1780882E-09 midg,1,midg; midg,igrid,midg -2.5138858E-09 8.3067020E-09 1,midg,midg; igrid,midg,midg 9.7146780E-09 -8.8827490E-10 gauss-seidel spectral radius is 0.9863241 estimated iterations to convergence 70 setup time was (sec) 0.6200000 now iterating at: 04:47:28 rms-change max change #iterations 0.1225729 17.88440 at 10iterations 1.1068944E-02 1.732188 at 20iterations 9.8044612E-04 0.1420898 at 30iterations 1.0517506E-04 1.8009186E-02 at 40iterations 2.2718374E-05 3.8175583E-03 at 50iterations finished qdiffx linear iterations at : 04:47:31 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 2.2718374E-05 3.8175583E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 04:47:32 4.070u 0.262s 0:04.60 94.1% 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 04:47:32 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2716 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: 1.844815 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): -10.63100 35.20500 ymin,ymax (A): 4.6000004E-02 57.93800 zmin,zma (A): -25.19700 27.23700 x,y,z range (A): 45.83600 57.89200 52.43400 scale (grids/A): 1.844815 object centre (A): 12.28700 28.99200 1.020000 number of atom coordinates read : 2716 total number of charged atoms : 2578 net assigned charge : 6.500036 assigned positive charge : 405.3073 centred at (gu) : 90.25598 86.37274 89.02896 assigned negative charge : -398.8084 centred at (gu) : 90.53129 86.04959 88.97910 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25862 grid for indexing accessible points = 1.400000 m= 24739 mr = 49570 m= 3605 mr = 16971 m= 193 mr = 1912 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 34603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20200 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) : 0.6149382 object centre at (A) : 12.28700 28.99200 1.020000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5075481E-03 -6.9958190E-03 midg,1,midg; midg,igrid,midg 6.6269515E-03 1.7946823E-02 1,midg,midg; igrid,midg,midg 2.1391215E-02 3.7673826E-03 gauss-seidel spectral radius is 0.9985703 estimated iterations to convergence 210 setup time was (sec) 0.9700000 now iterating at: 04:47:33 rms-change max change #iterations 4.077184 182.8641 at 10iterations 1.872108 70.87434 at 20iterations 0.8618838 28.44738 at 30iterations 0.3957988 13.35028 at 40iterations 0.1820816 6.166963 at 50iterations 8.3744764E-02 2.792282 at 60iterations 3.8612090E-02 1.213413 at 70iterations 1.7686496E-02 0.7244568 at 80iterations 8.1780190E-03 0.2521725 at 90iterations 3.7565234E-03 0.1377581 at 100iterations 1.7406688E-03 5.3689957E-02 at 110iterations 8.1456808E-04 2.4976730E-02 at 120iterations finished qdiffx linear iterations at : 04:47:41 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 8.1456808E-04 2.4976730E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 04:47:42 9.451u 0.281s 0:10.02 97.1% 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 04:47:42 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2716 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: 2.767222 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): -10.63100 35.20500 ymin,ymax (A): 4.6000004E-02 57.93800 zmin,zma (A): -25.19700 27.23700 x,y,z range (A): 45.83600 57.89200 52.43400 scale (grids/A): 2.767222 object centre (A): 12.28700 28.99200 1.020000 number of atom coordinates read : 2716 total number of charged atoms : 2578 net assigned charge : 6.500036 assigned positive charge : 405.3073 centred at (gu) : 90.38398 84.55882 88.54306 assigned negative charge : -398.8084 centred at (gu) : 90.79687 84.07430 88.46851 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 172714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25862 grid for indexing accessible points = 1.400000 m= 82239 mr = 121453 m= 27152 mr = 64449 m= 6113 mr = 20439 m= 815 mr = 4155 m= 42 mr = 468 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.700000 number of dielectric boundary points 78100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 20622 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) : 1.844815 object centre at (A) : 12.28700 28.99200 1.020000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1878247 -9.0440530E-03 midg,1,midg; midg,igrid,midg 9.4693499E-03 0.2099861 1,midg,midg; igrid,midg,midg 0.2031197 6.2939301E-02 gauss-seidel spectral radius is 0.9992533 estimated iterations to convergence 289 setup time was (sec) 2.050000 now iterating at: 04:47:44 rms-change max change #iterations 9.890791 350.7041 at 10iterations 5.829499 148.0340 at 20iterations 3.404553 72.27421 at 30iterations 1.972431 44.23249 at 40iterations 1.143208 24.29414 at 50iterations 0.6604049 12.25647 at 60iterations 0.3810361 8.083534 at 70iterations 0.2196263 4.366492 at 80iterations 0.1264034 2.644200 at 90iterations 7.2739445E-02 1.396904 at 100iterations 4.1712299E-02 0.8372209 at 110iterations 2.3944359E-02 0.4723053 at 120iterations 1.3742681E-02 0.2557807 at 130iterations 7.8990804E-03 0.1414680 at 140iterations 4.5353919E-03 8.1810951E-02 at 150iterations 2.6069982E-03 4.7166109E-02 at 160iterations 1.4985176E-03 2.8499126E-02 at 170iterations 8.6876046E-04 2.0000458E-02 at 180iterations finished qdiffx linear iterations at : 04:47:58 total time elapsed so far: 15.79000 # loops : 180 mean,max change (kT/e) : 8.6876046E-04 2.0000458E-02 energy calculations done at 15.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.97000 DelPhi exited at 04:47:58 15.971u 0.284s 0:16.50 98.4% 0+0k 0+0io 0pf+0w