Tue Oct 11 07:15:13 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 07:15:13 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5979576 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): 0.6569999 48.87000 ymin,ymax (A): -7.903000 49.36800 zmin,zma (A): 1.442000 60.97800 x,y,z range (A): 48.21300 57.27100 59.53600 scale (grids/A): 0.5979576 object centre (A): 24.76350 20.73250 31.21000 number of atom coordinates read : 3182 total number of charged atoms : 3040 net assigned charge : -0.9999901 assigned positive charge : 481.3919 centred at (gu) : 89.59428 89.21593 90.82862 assigned negative charge : -482.3930 centred at (gu) : 89.52219 89.13430 90.78658 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7555 nv = 96 ne = 84 npr = 64862 no. pairs analyzed = 64862 no. exposed pairs = 3856 no. arc points = 25907 no. surface atoms = 1313 nbur = 1869 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 4379 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3600000 number of dielectric boundary points 3510 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2586 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9468 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7919701E-09 1.7145098E-09 midg,1,midg; midg,igrid,midg -4.6461870E-09 2.5575726E-09 1,midg,midg; igrid,midg,midg -3.8011301E-09 2.4292262E-09 gauss-seidel spectral radius is 0.9855711 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 07:15:14 rms-change max change #iterations 0.1213189 22.88313 at 10iterations 1.1309543E-02 1.587471 at 20iterations 1.5702836E-03 0.2571831 at 30iterations 4.1876474E-04 7.6253891E-02 at 40iterations 1.3037348E-04 2.3843765E-02 at 50iterations finished qdiffx linear iterations at : 07:15:17 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.3037348E-04 2.3843765E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 07:15:18 3.547u 0.212s 0:04.19 89.4% 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 07:15:18 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.793873 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): 0.6569999 48.87000 ymin,ymax (A): -7.903000 49.36800 zmin,zma (A): 1.442000 60.97800 x,y,z range (A): 48.21300 57.27100 59.53600 scale (grids/A): 1.793873 object centre (A): 24.76350 20.73250 31.21000 number of atom coordinates read : 3182 total number of charged atoms : 3040 net assigned charge : -0.9999901 assigned positive charge : 481.3919 centred at (gu) : 88.78212 87.64724 92.48491 assigned negative charge : -482.3930 centred at (gu) : 88.56639 87.40262 92.35931 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 82556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25907 grid for indexing accessible points = 1.400000 m= 30260 mr = 59126 m= 4212 mr = 22873 m= 184 mr = 2618 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 32560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 23695 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) : 0.5979576 object centre at (A) : 24.76350 20.73250 31.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3277367E-03 1.0892911E-03 midg,1,midg; midg,igrid,midg -1.8574411E-02 1.1180962E-02 1,midg,midg; igrid,midg,midg -1.4064080E-02 2.4309643E-03 gauss-seidel spectral radius is 0.9985226 estimated iterations to convergence 206 setup time was (sec) 0.9400000 now iterating at: 07:15:19 rms-change max change #iterations 4.248141 187.7761 at 10iterations 1.933281 66.99158 at 20iterations 0.8800744 26.05993 at 30iterations 0.4013331 13.83238 at 40iterations 0.1834570 5.612495 at 50iterations 8.3590157E-02 2.499470 at 60iterations 3.8531210E-02 1.213409 at 70iterations 1.7613683E-02 0.5754547 at 80iterations 8.2239434E-03 0.2574081 at 90iterations 3.9496683E-03 0.1504829 at 100iterations 1.9672324E-03 6.6101074E-02 at 110iterations 1.0277793E-03 4.3590546E-02 at 120iterations finished qdiffx linear iterations at : 07:15:26 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.0277793E-03 4.3590546E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 07:15:27 8.076u 0.218s 0:08.80 94.0% 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 07:15:27 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.690809 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): 0.6569999 48.87000 ymin,ymax (A): -7.903000 49.36800 zmin,zma (A): 1.442000 60.97800 x,y,z range (A): 48.21300 57.27100 59.53600 scale (grids/A): 2.690809 object centre (A): 24.76350 20.73250 31.21000 number of atom coordinates read : 3182 total number of charged atoms : 3040 net assigned charge : -0.9999901 assigned positive charge : 481.3919 centred at (gu) : 88.17287 86.47070 93.72725 assigned negative charge : -482.3930 centred at (gu) : 87.84946 86.10389 93.53873 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 191548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25907 grid for indexing accessible points = 1.400000 m= 98786 mr = 143163 m= 34627 mr = 82100 m= 7289 mr = 28275 m= 752 mr = 5439 m= 23 mr = 468 m= 0 mr = 3 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.570000 number of dielectric boundary points 73577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 24312 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) : 1.793873 object centre at (A) : 24.76350 20.73250 31.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3089152 -0.2589015 midg,1,midg; midg,igrid,midg -0.3867624 0.1334424 1,midg,midg; igrid,midg,midg -0.1520274 5.9756623E-03 gauss-seidel spectral radius is 0.9992363 estimated iterations to convergence 286 setup time was (sec) 1.910000 now iterating at: 07:15:29 rms-change max change #iterations 10.20777 289.9778 at 10iterations 5.925644 124.7351 at 20iterations 3.411325 68.56314 at 30iterations 1.954391 37.36789 at 40iterations 1.121999 24.33565 at 50iterations 0.6420376 11.53499 at 60iterations 0.3667373 6.591167 at 70iterations 0.2095313 4.084300 at 80iterations 0.1196943 2.175766 at 90iterations 6.8459161E-02 1.182884 at 100iterations 3.8959410E-02 0.7108526 at 110iterations 2.2289762E-02 0.3734989 at 120iterations 1.2751608E-02 0.2231493 at 130iterations 7.3193037E-03 0.1293850 at 140iterations 4.2303731E-03 7.6263428E-02 at 150iterations 2.4815248E-03 4.7855377E-02 at 160iterations 1.4789820E-03 2.7107239E-02 at 170iterations 9.0852164E-04 1.8116951E-02 at 180iterations finished qdiffx linear iterations at : 07:15:40 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 9.0852164E-04 1.8116951E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 07:15:40 13.253u 0.233s 0:13.76 97.9% 0+0k 0+0io 0pf+0w