Tue Nov 22 14:12:06 PST 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 Tue Nov 22 2011 at 14:12:07 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6245505 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): -35.22900 9.970000 ymin,ymax (A): 1.318000 42.45700 zmin,zma (A): -1.816000 55.18500 x,y,z range (A): 45.19900 41.13900 57.00100 scale (grids/A): 0.6245505 object centre (A): -12.62950 21.88750 26.68450 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 291.4219 centred at (gu) : 90.42560 89.19324 90.74436 assigned negative charge : -288.4222 centred at (gu) : 90.36829 89.31866 90.76066 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5216 nv = 96 ne = 84 npr = 40015 no. pairs analyzed = 40015 no. exposed pairs = 2471 no. arc points = 16911 no. surface atoms = 839 nbur = 1121 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 293 mr = 2898 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1688 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6167 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0883209E-09 2.0801414E-09 midg,1,midg; midg,igrid,midg 1.1548334E-08 -3.7012235E-09 1,midg,midg; igrid,midg,midg -4.8044940E-10 6.4832522E-09 gauss-seidel spectral radius is 0.9866670 estimated iterations to convergence 71 setup time was (sec) 0.4400000 now iterating at: 14:12:09 rms-change max change #iterations 0.1149677 18.38375 at 10iterations 1.0553545E-02 1.953053 at 20iterations 9.8186661E-04 0.1575845 at 30iterations 8.9346904E-05 1.5579224E-02 at 40iterations 8.4905932E-06 1.2931824E-03 at 50iterations finished qdiffx linear iterations at : 14:12:19 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 8.4905932E-06 1.2931824E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 14:12:20 3.228u 0.198s 0:12.92 26.3% 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 Tue Nov 22 2011 at 14:12:22 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.873651 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): -35.22900 9.970000 ymin,ymax (A): 1.318000 42.45700 zmin,zma (A): -1.816000 55.18500 x,y,z range (A): 45.19900 41.13900 57.00100 scale (grids/A): 1.873651 object centre (A): -12.62950 21.88750 26.68450 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 291.4219 centred at (gu) : 91.27660 87.57977 92.23327 assigned negative charge : -288.4222 centred at (gu) : 91.10505 87.95613 92.28214 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 55801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16911 grid for indexing accessible points = 1.400000 m= 21021 mr = 38416 m= 3507 mr = 15999 m= 197 mr = 2422 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 378 time to turn everything in is 0.4000000 number of dielectric boundary points 23618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14330 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) : 0.6245505 object centre at (A) : -12.62950 21.88750 26.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4903271E-02 3.6577966E-02 midg,1,midg; midg,igrid,midg 3.6701718E-03 -7.4401498E-03 1,midg,midg; igrid,midg,midg -2.6282489E-03 -1.9459776E-03 gauss-seidel spectral radius is 0.9985147 estimated iterations to convergence 206 setup time was (sec) 0.6800000 now iterating at: 14:12:23 rms-change max change #iterations 3.489799 166.9017 at 10iterations 1.580570 60.91108 at 20iterations 0.7160763 26.83250 at 30iterations 0.3252143 12.44697 at 40iterations 0.1473324 5.467445 at 50iterations 6.6642545E-02 2.331291 at 60iterations 3.0227592E-02 1.179794 at 70iterations 1.3719057E-02 0.4888344 at 80iterations 6.1943289E-03 0.2133474 at 90iterations 2.8120312E-03 0.1022186 at 100iterations 1.2767797E-03 5.0533652E-02 at 110iterations 5.7733577E-04 2.0332336E-02 at 120iterations finished qdiffx linear iterations at : 14:12:40 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 5.7733577E-04 2.0332336E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 14:12:41 6.979u 0.178s 0:19.37 36.8% 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 Tue Nov 22 2011 at 14:12:45 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.810477 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): -35.22900 9.970000 ymin,ymax (A): 1.318000 42.45700 zmin,zma (A): -1.816000 55.18500 x,y,z range (A): 45.19900 41.13900 57.00100 scale (grids/A): 2.810477 object centre (A): -12.62950 21.88750 26.68450 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 291.4219 centred at (gu) : 91.91485 86.36964 93.34978 assigned negative charge : -288.4222 centred at (gu) : 91.65768 86.93405 93.42319 start vw surface at 0.1200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 128713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16911 grid for indexing accessible points = 1.400000 m= 67271 mr = 92815 m= 25591 mr = 55811 m= 6287 mr = 21352 m= 877 mr = 5026 m= 65 mr = 642 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 1411 time to turn everything in is 0.9800000 number of dielectric boundary points 53130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 14624 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) : 1.873651 object centre at (A) : -12.62950 21.88750 26.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2037032E-02 0.2469325 midg,1,midg; midg,igrid,midg -3.6237773E-02 -9.1769353E-02 1,midg,midg; igrid,midg,midg -6.1168145E-02 -4.7006164E-02 gauss-seidel spectral radius is 0.9992090 estimated iterations to convergence 281 setup time was (sec) 1.260000 now iterating at: 14:12:52 rms-change max change #iterations 8.260097 300.7228 at 10iterations 4.726194 152.4626 at 20iterations 2.671108 59.89564 at 30iterations 1.519341 32.21934 at 40iterations 0.8567792 18.39043 at 50iterations 0.4828828 11.69581 at 60iterations 0.2720039 5.734550 at 70iterations 0.1534079 3.059944 at 80iterations 8.6386912E-02 1.674864 at 90iterations 4.8614774E-02 0.9430103 at 100iterations 2.7367109E-02 0.5846405 at 110iterations 1.5396727E-02 0.3021936 at 120iterations 8.6667519E-03 0.1873493 at 130iterations 4.8751268E-03 0.1028118 at 140iterations 2.7417056E-03 6.5609634E-02 at 150iterations 1.5435320E-03 3.0615807E-02 at 160iterations 8.6806522E-04 1.7430067E-02 at 170iterations 4.8765558E-04 1.1357784E-02 at 180iterations finished qdiffx linear iterations at : 14:13:25 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 4.8765558E-04 1.1357784E-02 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 14:13:30 12.131u 0.168s 0:45.54 26.9% 0+0k 0+0io 0pf+0w