Mon Oct 10 19:35:03 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 Mon Oct 10 2011 at 19:35:03 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 = 2451 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: 0.6204793 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): 10.39300 67.76800 ymin,ymax (A): 49.04400 99.91400 zmin,zma (A): -26.83200 24.19700 x,y,z range (A): 57.37500 50.87000 51.02900 scale (grids/A): 0.6204793 object centre (A): 39.08050 74.47900 -1.317499 number of atom coordinates read : 2451 total number of charged atoms : 2312 net assigned charge : 5.000029 assigned positive charge : 359.0140 centred at (gu) : 90.97491 88.54049 91.53918 assigned negative charge : -354.0150 centred at (gu) : 91.08861 88.53500 91.51164 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6270 nv = 96 ne = 84 npr = 50037 no. pairs analyzed = 50037 no. exposed pairs = 3140 no. arc points = 22376 no. surface atoms = 1063 nbur = 1388 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 323 mr = 3271 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2283 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7705 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7771978E-09 8.1068219E-09 midg,1,midg; midg,igrid,midg 5.1643307E-09 3.2681566E-09 1,midg,midg; igrid,midg,midg 8.8692058E-09 -3.6984649E-09 gauss-seidel spectral radius is 0.9865404 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 19:35:03 rms-change max change #iterations 0.1216858 18.58307 at 10iterations 1.1276726E-02 1.793543 at 20iterations 1.0610999E-03 0.1764469 at 30iterations 1.1776653E-04 1.6828537E-02 at 40iterations 1.8715938E-05 3.3693314E-03 at 50iterations finished qdiffx linear iterations at : 19:35:07 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 1.8715938E-05 3.3693314E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 19:35:08 4.139u 0.263s 0:04.90 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 Mon Oct 10 2011 at 19:35:08 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 = 2451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.861438 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): 10.39300 67.76800 ymin,ymax (A): 49.04400 99.91400 zmin,zma (A): -26.83200 24.19700 x,y,z range (A): 57.37500 50.87000 51.02900 scale (grids/A): 1.861438 object centre (A): 39.08050 74.47900 -1.317499 number of atom coordinates read : 2451 total number of charged atoms : 2312 net assigned charge : 5.000029 assigned positive charge : 359.0140 centred at (gu) : 92.92420 85.62093 94.61709 assigned negative charge : -354.0150 centred at (gu) : 93.26588 85.60510 94.53494 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 68160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22376 grid for indexing accessible points = 1.400000 m= 22869 mr = 45747 m= 3156 mr = 16322 m= 165 mr = 1777 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 30466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 18118 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) : 0.6204793 object centre at (A) : 39.08050 74.47900 -1.317499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1421725E-02 2.6784606E-02 midg,1,midg; midg,igrid,midg 2.4085417E-02 7.0405155E-03 1,midg,midg; igrid,midg,midg 1.4218291E-02 -4.0018797E-02 gauss-seidel spectral radius is 0.9985627 estimated iterations to convergence 209 setup time was (sec) 0.9100000 now iterating at: 19:35:09 rms-change max change #iterations 3.875429 166.8768 at 10iterations 1.767277 58.84357 at 20iterations 0.8115774 26.83567 at 30iterations 0.3719918 12.26069 at 40iterations 0.1709988 5.704966 at 50iterations 7.8326881E-02 2.630257 at 60iterations 3.5991348E-02 1.306175 at 70iterations 1.6475728E-02 0.5645351 at 80iterations 7.5714611E-03 0.2410545 at 90iterations 3.4837509E-03 0.1192487 at 100iterations 1.6002177E-03 5.9102058E-02 at 110iterations 7.3855137E-04 2.3842096E-02 at 120iterations finished qdiffx linear iterations at : 19:35:17 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 7.3855137E-04 2.3842096E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 19:35:18 9.577u 0.329s 0:10.55 93.7% 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 Mon Oct 10 2011 at 19:35:18 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 = 2451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.792157 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): 10.39300 67.76800 ymin,ymax (A): 49.04400 99.91400 zmin,zma (A): -26.83200 24.19700 x,y,z range (A): 57.37500 50.87000 51.02900 scale (grids/A): 2.792157 object centre (A): 39.08050 74.47900 -1.317499 number of atom coordinates read : 2451 total number of charged atoms : 2312 net assigned charge : 5.000029 assigned positive charge : 359.0140 centred at (gu) : 94.38628 83.43118 96.92564 assigned negative charge : -354.0150 centred at (gu) : 94.89870 83.40768 96.80244 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 157770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22376 grid for indexing accessible points = 1.400000 m= 75236 mr = 111658 m= 25617 mr = 60153 m= 5311 mr = 20089 m= 665 mr = 3739 m= 54 mr = 410 m= 0 mr = 17 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 68587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 18493 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) : 1.861438 object centre at (A) : 39.08050 74.47900 -1.317499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5224814 0.2263976 midg,1,midg; midg,igrid,midg 0.3479862 7.4493788E-02 1,midg,midg; igrid,midg,midg 0.2576837 -0.4632372 gauss-seidel spectral radius is 0.9992426 estimated iterations to convergence 287 setup time was (sec) 1.890000 now iterating at: 19:35:20 rms-change max change #iterations 9.303014 299.8718 at 10iterations 5.432893 143.4306 at 20iterations 3.148279 74.57420 at 30iterations 1.829818 42.97571 at 40iterations 1.053629 23.35706 at 50iterations 0.6043261 12.81171 at 60iterations 0.3473677 6.915123 at 70iterations 0.1993696 3.833505 at 80iterations 0.1141033 2.222256 at 90iterations 6.5259628E-02 1.189623 at 100iterations 3.7420917E-02 0.8563499 at 110iterations 2.1398155E-02 0.3868942 at 120iterations 1.2265095E-02 0.2406254 at 130iterations 7.0258034E-03 0.1347558 at 140iterations 4.0361001E-03 8.2183838E-02 at 150iterations 2.3302166E-03 4.9324751E-02 at 160iterations 1.3495240E-03 2.5136590E-02 at 170iterations 7.9415360E-04 1.6076565E-02 at 180iterations finished qdiffx linear iterations at : 19:35:34 total time elapsed so far: 15.80000 # loops : 180 mean,max change (kT/e) : 7.9415360E-04 1.6076565E-02 energy calculations done at 15.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.98000 DelPhi exited at 19:35:35 15.986u 0.314s 0:16.59 98.1% 0+0k 0+0io 0pf+0w