Sun Oct 9 03:49:09 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 Sun Oct 9 2011 at 03:49:09 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5523 !!! WARNING: SEP 530 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5074551 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): -2.963000 64.49100 ymin,ymax (A): -10.99900 59.15500 zmin,zma (A): -19.81400 41.94200 x,y,z range (A): 67.45399 70.15400 61.75600 scale (grids/A): 0.5074551 object centre (A): 30.76400 24.07800 11.06400 number of atom coordinates read : 5523 total number of charged atoms : 5363 net assigned charge : 16.52496 assigned positive charge : 842.0775 centred at (gu) : 90.06580 92.09658 89.82150 assigned negative charge : -825.5603 centred at (gu) : 90.00234 92.14020 89.79266 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8377 nv = 96 ne = 84 npr = 114099 no. pairs analyzed = 114099 no. exposed pairs = 7409 no. arc points = 50238 no. surface atoms = 2475 nbur = 3048 mkacc time = 0.2400000 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 = 1.708000 m= 286 mr = 3911 m= 0 mr = 7 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4807 ## 697 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11733 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3583876E-10 2.6732638E-10 midg,1,midg; midg,igrid,midg 1.8507693E-10 1.5224895E-10 1,midg,midg; igrid,midg,midg 3.8050427E-11 3.7555364E-10 gauss-seidel spectral radius is 0.9801862 estimated iterations to convergence 59 setup time was (sec) 0.7500000 now iterating at: 03:49:10 rms-change max change #iterations 7.4263990E-02 10.84335 at 10iterations 6.0078213E-03 0.8066826 at 20iterations 1.5342899E-03 0.2078743 at 30iterations 5.1673834E-04 6.4243317E-02 at 40iterations 1.7753958E-04 2.0927429E-02 at 50iterations finished qdiffx linear iterations at : 03:49:12 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.7753958E-04 2.0927429E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 03:49:13 3.585u 0.209s 0:04.13 91.5% 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 03:49:13 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5523 !!! WARNING: SEP 530 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.522365 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): -2.963000 64.49100 ymin,ymax (A): -10.99900 59.15500 zmin,zma (A): -19.81400 41.94200 x,y,z range (A): 67.45399 70.15400 61.75600 scale (grids/A): 1.522365 object centre (A): 30.76400 24.07800 11.06400 number of atom coordinates read : 5523 total number of charged atoms : 5363 net assigned charge : 16.52496 assigned positive charge : 842.0775 centred at (gu) : 90.19513 96.28739 89.46233 assigned negative charge : -825.5603 centred at (gu) : 90.00676 96.41998 89.37776 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 93089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50238 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 25644 mr = 59789 m= 2206 mr = 16082 m= 36 mr = 886 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 44216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 621 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 40273 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) : 0.5074551 object centre at (A) : 30.76400 24.07800 11.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7088593E-03 1.1230802E-02 midg,1,midg; midg,igrid,midg 3.2379359E-02 4.2105768E-02 1,midg,midg; igrid,midg,midg -1.0330833E-02 1.2846270E-02 gauss-seidel spectral radius is 0.9981526 estimated iterations to convergence 185 setup time was (sec) 0.9700000 now iterating at: 03:49:14 rms-change max change #iterations 4.087389 164.6168 at 10iterations 1.681320 49.27430 at 20iterations 0.6945323 22.68435 at 30iterations 0.2877941 9.401962 at 40iterations 0.1191184 3.859217 at 50iterations 4.9562350E-02 1.577137 at 60iterations 2.0884695E-02 0.6967673 at 70iterations 8.9829611E-03 0.2763605 at 80iterations 4.0736888E-03 0.1338730 at 90iterations 2.0308993E-03 6.5879822E-02 at 100iterations 1.1306413E-03 3.6804199E-02 at 110iterations 6.9038715E-04 2.3426056E-02 at 120iterations finished qdiffx linear iterations at : 03:49:21 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 6.9038715E-04 2.3426056E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 03:49:22 8.002u 0.242s 0:08.53 96.6% 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 03:49:22 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5523 !!! WARNING: SEP 530 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.283548 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): -2.963000 64.49100 ymin,ymax (A): -10.99900 59.15500 zmin,zma (A): -19.81400 41.94200 x,y,z range (A): 67.45399 70.15400 61.75600 scale (grids/A): 2.283548 object centre (A): 30.76400 24.07800 11.06400 number of atom coordinates read : 5523 total number of charged atoms : 5363 net assigned charge : 16.52496 assigned positive charge : 842.0775 centred at (gu) : 90.29209 99.43039 89.19304 assigned negative charge : -825.5603 centred at (gu) : 90.00996 99.62983 89.06633 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 216961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50238 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 90899 mr = 148943 m= 23114 mr = 67305 m= 3060 mr = 16312 m= 125 mr = 1765 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 99798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 42760 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) : 1.522365 object centre at (A) : 30.76400 24.07800 11.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1960042E-02 0.1669257 midg,1,midg; midg,igrid,midg 0.9156649 0.6463390 1,midg,midg; igrid,midg,midg -0.2648052 0.2965459 gauss-seidel spectral radius is 0.9991965 estimated iterations to convergence 279 setup time was (sec) 1.940000 now iterating at: 03:49:24 rms-change max change #iterations 11.26779 265.5660 at 10iterations 6.594566 159.7096 at 20iterations 3.825567 82.18100 at 30iterations 2.202071 51.64554 at 40iterations 1.262197 29.20800 at 50iterations 0.7214211 14.88250 at 60iterations 0.4097980 8.283833 at 70iterations 0.2325086 4.628637 at 80iterations 0.1319294 2.586582 at 90iterations 7.4586384E-02 1.505056 at 100iterations 4.2120062E-02 0.8856401 at 110iterations 2.3834722E-02 0.4758720 at 120iterations 1.3494322E-02 0.2418823 at 130iterations 7.6612518E-03 0.1496468 at 140iterations 4.3750689E-03 7.7193260E-02 at 150iterations 2.5228264E-03 4.6672821E-02 at 160iterations 1.4794306E-03 2.8564453E-02 at 170iterations 8.8773755E-04 1.5739441E-02 at 180iterations finished qdiffx linear iterations at : 03:49:35 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 8.8773755E-04 1.5739441E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 03:49:36 13.437u 0.252s 0:14.29 95.7% 0+0k 0+0io 0pf+0w