Sun Oct 9 17:15:10 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 Sun Oct 9 2011 at 17:15:10 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5027 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5640497 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): 3.245000 64.97500 ymin,ymax (A): -8.570000 53.44800 zmin,zma (A): -1.178000 61.93700 x,y,z range (A): 61.73000 62.01800 63.11500 scale (grids/A): 0.5640497 object centre (A): 34.11000 22.43900 30.37950 number of atom coordinates read : 5027 total number of charged atoms : 4878 net assigned charge : 0.1210471 assigned positive charge : 771.1458 centred at (gu) : 88.34906 89.24677 89.20247 assigned negative charge : -771.0305 centred at (gu) : 88.24569 89.28323 89.17323 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 10491 nv = 96 ne = 84 npr = 101958 no. pairs analyzed = 101958 no. exposed pairs = 5935 no. arc points = 40072 no. surface atoms = 2023 nbur = 3004 mkacc time = 0.2600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 507 mr = 6056 m= 1 mr = 23 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 0.5300000 number of dielectric boundary points 4920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4090 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 13689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1824091E-10 5.7651339E-10 midg,1,midg; midg,igrid,midg 1.0320185E-09 -6.2490269E-10 1,midg,midg; igrid,midg,midg -3.3885126E-09 1.5490580E-09 gauss-seidel spectral radius is 0.9839368 estimated iterations to convergence 65 setup time was (sec) 0.8400000 now iterating at: 17:15:11 rms-change max change #iterations 0.1177638 14.05805 at 10iterations 1.0906097E-02 1.432491 at 20iterations 3.0253273E-03 0.3330841 at 30iterations 1.4293920E-03 0.1523528 at 40iterations 7.0726417E-04 8.2048893E-02 at 50iterations finished qdiffx linear iterations at : 17:15:16 total time elapsed so far: 5.510000 # loops : 50 mean,max change (kT/e) : 7.0726417E-04 8.2048893E-02 energy calculations done at 5.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.680000 DelPhi exited at 17:15:16 5.684u 0.485s 0:06.59 93.4% 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 Sun Oct 9 2011 at 17:15:16 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5027 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.692149 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): 3.245000 64.97500 ymin,ymax (A): -8.570000 53.44800 zmin,zma (A): -1.178000 61.93700 x,y,z range (A): 61.73000 62.01800 63.11500 scale (grids/A): 1.692149 object centre (A): 34.11000 22.43900 30.37950 number of atom coordinates read : 5027 total number of charged atoms : 4878 net assigned charge : 0.1210471 assigned positive charge : 771.1458 centred at (gu) : 85.04584 87.73905 87.60580 assigned negative charge : -771.0305 centred at (gu) : 84.73703 87.84994 87.51976 start vw surface at 0.1800000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 116753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40072 grid for indexing accessible points = 1.400000 m= 41239 mr = 84561 m= 5303 mr = 29953 m= 182 mr = 2972 m= 0 mr = 27 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 45964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 370 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 37597 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) : 0.5640497 object centre at (A) : 34.11000 22.43900 30.37950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0380188E-02 -2.8809801E-02 midg,1,midg; midg,igrid,midg 1.7439531E-02 9.9042691E-03 1,midg,midg; igrid,midg,midg -2.0154396E-02 2.7549986E-02 gauss-seidel spectral radius is 0.9985006 estimated iterations to convergence 205 setup time was (sec) 1.370000 now iterating at: 17:15:18 rms-change max change #iterations 4.992132 194.0145 at 10iterations 2.246565 64.72093 at 20iterations 1.016532 28.97336 at 30iterations 0.4614406 12.85728 at 40iterations 0.2085548 5.784486 at 50iterations 9.4953954E-02 2.584663 at 60iterations 4.3392722E-02 1.278286 at 70iterations 2.0305187E-02 0.5511017 at 80iterations 9.9952063E-03 0.2990875 at 90iterations 5.4661874E-03 0.1483002 at 100iterations 3.4106383E-03 9.4978333E-02 at 110iterations 2.4040441E-03 6.1481476E-02 at 120iterations finished qdiffx linear iterations at : 17:15:30 total time elapsed so far: 13.43000 # loops : 120 mean,max change (kT/e) : 2.4040441E-03 6.1481476E-02 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 17:15:31 13.617u 0.537s 0:14.47 97.7% 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 Sun Oct 9 2011 at 17:15:31 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5027 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.538224 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): 3.245000 64.97500 ymin,ymax (A): -8.570000 53.44800 zmin,zma (A): -1.178000 61.93700 x,y,z range (A): 61.73000 62.01800 63.11500 scale (grids/A): 2.538224 object centre (A): 34.11000 22.43900 30.37950 number of atom coordinates read : 5027 total number of charged atoms : 4878 net assigned charge : 0.1210471 assigned positive charge : 771.1458 centred at (gu) : 82.56861 86.60809 86.40832 assigned negative charge : -771.0305 centred at (gu) : 82.10537 86.77489 86.27956 start vw surface at 0.2000000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 271168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40072 grid for indexing accessible points = 1.400000 m= 138203 mr = 205729 m= 45135 mr = 112850 m= 8798 mr = 35168 m= 817 mr = 6166 m= 27 mr = 421 m= 0 mr = 4 time to grow re-entrant surface = 1.620000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.540000 number of dielectric boundary points 103810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 2.740000 number of grid points assigned charge 38994 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) : 1.692149 object centre at (A) : 34.11000 22.43900 30.37950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4751328 -0.6737664 midg,1,midg; midg,igrid,midg -1.3082698E-02 2.1977723E-03 1,midg,midg; igrid,midg,midg -0.3982626 0.3119282 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 2.970000 now iterating at: 17:15:34 rms-change max change #iterations 12.54783 320.8932 at 10iterations 7.444357 140.9581 at 20iterations 4.397602 87.77444 at 30iterations 2.586813 45.56130 at 40iterations 1.515909 28.50221 at 50iterations 0.8860441 15.36728 at 60iterations 0.5163643 7.669264 at 70iterations 0.3009508 4.593220 at 80iterations 0.1750634 2.956151 at 90iterations 0.1017227 1.753769 at 100iterations 5.9131313E-02 0.9558840 at 110iterations 3.4556899E-02 0.5585175 at 120iterations 2.0260831E-02 0.3125553 at 130iterations 1.2070128E-02 0.1988678 at 140iterations 7.3841978E-03 0.1125031 at 150iterations 4.7414615E-03 7.9982758E-02 at 160iterations 3.2597764E-03 5.0903320E-02 at 170iterations 2.4157751E-03 3.5900116E-02 at 180iterations finished qdiffx linear iterations at : 17:15:56 total time elapsed so far: 24.58000 # loops : 180 mean,max change (kT/e) : 2.4157751E-03 3.5900116E-02 energy calculations done at 24.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.75000 DelPhi exited at 17:15:56 24.760u 0.567s 0:25.62 98.8% 0+0k 0+0io 0pf+0w