Tue Oct 11 03:14:09 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 Tue Oct 11 2011 at 03:14:09 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3411 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: HIR 298 has a net charge of 0.5140 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: 0.5393448 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): -43.06200 11.31600 ymin,ymax (A): -55.27600 3.628000 zmin,zma (A): -34.27200 31.73400 x,y,z range (A): 54.37800 58.90400 66.00600 scale (grids/A): 0.5393448 object centre (A): -15.87300 -25.82400 -1.269001 number of atom coordinates read : 3411 total number of charged atoms : 3266 net assigned charge : -8.079977 assigned positive charge : 519.1622 centred at (gu) : 91.75497 87.92016 92.24672 assigned negative charge : -527.2438 centred at (gu) : 91.70702 87.90901 92.28145 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6352 nv = 96 ne = 84 npr = 69687 no. pairs analyzed = 69687 no. exposed pairs = 4233 no. arc points = 29879 no. surface atoms = 1410 nbur = 2001 mkacc time = 0.1200000 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 = 1.596000 m= 293 mr = 3344 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3042 ## 435 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0289115E-10 -1.0349717E-09 midg,1,midg; midg,igrid,midg -7.4757861E-10 -1.9060878E-10 1,midg,midg; igrid,midg,midg -4.3580284E-10 -1.3234409E-10 gauss-seidel spectral radius is 0.9823126 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 03:14:10 rms-change max change #iterations 7.6876298E-02 13.19500 at 10iterations 5.3196223E-03 0.7965631 at 20iterations 5.3272082E-04 8.2902908E-02 at 30iterations 1.1417208E-04 1.4684677E-02 at 40iterations 3.0201378E-05 3.7727356E-03 at 50iterations finished qdiffx linear iterations at : 03:14:13 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.0201378E-05 3.7727356E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 03:14:14 3.478u 0.172s 0:04.13 88.1% 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 Tue Oct 11 2011 at 03:14:14 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3411 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: HIR 298 has a net charge of 0.5140 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: 1.618035 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): -43.06200 11.31600 ymin,ymax (A): -55.27600 3.628000 zmin,zma (A): -34.27200 31.73400 x,y,z range (A): 54.37800 58.90400 66.00600 scale (grids/A): 1.618035 object centre (A): -15.87300 -25.82400 -1.269001 number of atom coordinates read : 3411 total number of charged atoms : 3266 net assigned charge : -8.079977 assigned positive charge : 519.1622 centred at (gu) : 95.26388 83.75932 96.73905 assigned negative charge : -527.2438 centred at (gu) : 95.12061 83.72666 96.84363 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 71291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29879 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21690 mr = 48653 m= 2244 mr = 14798 m= 71 mr = 1061 m= 0 mr = 6 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 684 time to turn everything in is 0.3700000 number of dielectric boundary points 30778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 419 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 24893 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) : 0.5393448 object centre at (A) : -15.87300 -25.82400 -1.269001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4527861E-02 -1.4365835E-02 midg,1,midg; midg,igrid,midg -5.2227164E-03 -4.6360171E-03 1,midg,midg; igrid,midg,midg -5.6885304E-03 -4.2559388E-03 gauss-seidel spectral radius is 0.9981849 estimated iterations to convergence 186 setup time was (sec) 0.5800000 now iterating at: 03:14:14 rms-change max change #iterations 3.584853 160.9933 at 10iterations 1.493987 56.25449 at 20iterations 0.6237977 22.55902 at 30iterations 0.2594792 8.661011 at 40iterations 0.1086559 3.923187 at 50iterations 4.5104612E-02 1.693110 at 60iterations 1.8876594E-02 0.6431494 at 70iterations 7.9262853E-03 0.2700958 at 80iterations 3.3641479E-03 0.1138916 at 90iterations 1.4499328E-03 4.9529552E-02 at 100iterations 6.4909353E-04 2.2798657E-02 at 110iterations 3.0315237E-04 1.2719393E-02 at 120iterations finished qdiffx linear iterations at : 03:14:21 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 3.0315237E-04 1.2719393E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 03:14:22 7.800u 0.206s 0:08.38 95.4% 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 Oct 11 2011 at 03:14:22 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3411 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: HIR 298 has a net charge of 0.5140 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: 2.427052 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): -43.06200 11.31600 ymin,ymax (A): -55.27600 3.628000 zmin,zma (A): -34.27200 31.73400 x,y,z range (A): 54.37800 58.90400 66.00600 scale (grids/A): 2.427052 object centre (A): -15.87300 -25.82400 -1.269001 number of atom coordinates read : 3411 total number of charged atoms : 3266 net assigned charge : -8.079977 assigned positive charge : 519.1622 centred at (gu) : 97.89584 80.63857 100.1083 assigned negative charge : -527.2438 centred at (gu) : 97.68058 80.58994 100.2653 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 166055 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29879 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 75629 mr = 119311 m= 20999 mr = 59806 m= 3539 mr = 15594 m= 239 mr = 2295 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2135 time to turn everything in is 0.8700000 number of dielectric boundary points 69386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 26102 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) : 1.618035 object centre at (A) : -15.87300 -25.82400 -1.269001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4725951 -0.3445586 midg,1,midg; midg,igrid,midg -2.8094742E-02 -7.5546671E-03 1,midg,midg; igrid,midg,midg -9.3156837E-02 -4.0249798E-02 gauss-seidel spectral radius is 0.9991445 estimated iterations to convergence 270 setup time was (sec) 1.100000 now iterating at: 03:14:23 rms-change max change #iterations 9.343509 255.0490 at 10iterations 5.272106 153.1510 at 20iterations 2.953169 67.36068 at 30iterations 1.653496 41.11754 at 40iterations 0.9190020 24.77767 at 50iterations 0.5103174 10.78305 at 60iterations 0.2826409 5.838357 at 70iterations 0.1565272 3.279633 at 80iterations 8.6741894E-02 1.776276 at 90iterations 4.7864724E-02 0.9785135 at 100iterations 2.6417414E-02 0.5521812 at 110iterations 1.4604761E-02 0.3274193 at 120iterations 8.0714002E-03 0.1636729 at 130iterations 4.4722720E-03 8.0942154E-02 at 140iterations 2.4848275E-03 5.3169250E-02 at 150iterations 1.3870614E-03 2.8686523E-02 at 160iterations 7.7882170E-04 1.4415741E-02 at 170iterations 4.4375658E-04 8.6688995E-03 at 180iterations finished qdiffx linear iterations at : 03:14:35 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 4.4375658E-04 8.6688995E-03 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 03:14:35 12.502u 0.220s 0:13.06 97.3% 0+0k 0+0io 0pf+0w