Mon Oct 10 14:40:05 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 Mon Oct 10 2011 at 14:40:05 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6577610 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): -22.75500 31.36800 ymin,ymax (A): 12.15600 58.13100 zmin,zma (A): 28.07900 78.25800 x,y,z range (A): 54.12300 45.97500 50.17900 scale (grids/A): 0.6577610 object centre (A): 4.306500 35.14350 53.16850 number of atom coordinates read : 2377 total number of charged atoms : 2244 net assigned charge : -2.499994 assigned positive charge : 360.8772 centred at (gu) : 89.64671 90.73811 90.29198 assigned negative charge : -363.3778 centred at (gu) : 89.85964 90.70980 90.38888 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6904 nv = 96 ne = 84 npr = 49259 no. pairs analyzed = 49259 no. exposed pairs = 2939 no. arc points = 20683 no. surface atoms = 1006 nbur = 1371 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3840 m= 0 mr = 64 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.2000000 number of dielectric boundary points 3405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2009 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8169 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0048003E-08 -2.4648079E-08 midg,1,midg; midg,igrid,midg -9.4706998E-09 -1.2549682E-09 1,midg,midg; igrid,midg,midg 3.2748797E-08 -4.0978865E-08 gauss-seidel spectral radius is 0.9880028 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 14:40:06 rms-change max change #iterations 0.1607709 30.19318 at 10iterations 1.7076518E-02 2.484636 at 20iterations 1.7845839E-03 0.2775116 at 30iterations 2.1297747E-04 2.8316498E-02 at 40iterations 3.2823398E-05 5.4397583E-03 at 50iterations finished qdiffx linear iterations at : 14:40:09 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.2823398E-05 5.4397583E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:40:09 3.397u 0.160s 0:04.07 87.2% 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 14:40:09 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.973283 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): -22.75500 31.36800 ymin,ymax (A): 12.15600 58.13100 zmin,zma (A): 28.07900 78.25800 x,y,z range (A): 54.12300 45.97500 50.17900 scale (grids/A): 1.973283 object centre (A): 4.306500 35.14350 53.16850 number of atom coordinates read : 2377 total number of charged atoms : 2244 net assigned charge : -2.499994 assigned positive charge : 360.8772 centred at (gu) : 88.93944 92.21399 90.87548 assigned negative charge : -363.3778 centred at (gu) : 89.57877 92.12941 91.16638 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74619 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20683 grid for indexing accessible points = 1.400000 m= 27857 mr = 51922 m= 5137 mr = 20801 m= 446 mr = 3435 m= 9 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1102 time to turn everything in is 0.3900000 number of dielectric boundary points 31688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17736 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) : 0.6577610 object centre at (A) : 4.306500 35.14350 53.16850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1615406E-02 -3.2858517E-02 midg,1,midg; midg,igrid,midg -1.0748198E-02 2.3545981E-03 1,midg,midg; igrid,midg,midg 4.5430161E-02 -1.0346745E-02 gauss-seidel spectral radius is 0.9987057 estimated iterations to convergence 220 setup time was (sec) 0.6000000 now iterating at: 14:40:10 rms-change max change #iterations 4.425708 198.0347 at 10iterations 2.110128 74.41851 at 20iterations 1.003858 31.88485 at 30iterations 0.4801930 14.03950 at 40iterations 0.2289061 7.678447 at 50iterations 0.1093465 3.535168 at 60iterations 5.2397225E-02 1.719513 at 70iterations 2.5013451E-02 0.7659760 at 80iterations 1.1961405E-02 0.3693657 at 90iterations 5.7298001E-03 0.2066956 at 100iterations 2.7413408E-03 9.0492249E-02 at 110iterations 1.3199882E-03 3.8391113E-02 at 120iterations finished qdiffx linear iterations at : 14:40:17 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.3199882E-03 3.8391113E-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) 7.810000 DelPhi exited at 14:40:18 7.810u 0.194s 0:08.29 96.5% 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 Mon Oct 10 2011 at 14:40:18 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.959924 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): -22.75500 31.36800 ymin,ymax (A): 12.15600 58.13100 zmin,zma (A): 28.07900 78.25800 x,y,z range (A): 54.12300 45.97500 50.17900 scale (grids/A): 2.959924 object centre (A): 4.306500 35.14350 53.16850 number of atom coordinates read : 2377 total number of charged atoms : 2244 net assigned charge : -2.499994 assigned positive charge : 360.8772 centred at (gu) : 88.40910 93.32095 91.31319 assigned negative charge : -363.3778 centred at (gu) : 89.36809 93.19405 91.74949 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 172676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20683 grid for indexing accessible points = 1.400000 m= 88131 mr = 125849 m= 34220 mr = 72457 m= 9527 mr = 28024 m= 1863 mr = 7436 m= 173 mr = 1394 m= 7 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 3589 time to turn everything in is 0.9800000 number of dielectric boundary points 71352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 17951 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) : 1.973283 object centre at (A) : 4.306500 35.14350 53.16850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3369280 -0.1794368 midg,1,midg; midg,igrid,midg -4.4356059E-02 9.9662825E-02 1,midg,midg; igrid,midg,midg 0.5663617 -1.9298891E-02 gauss-seidel spectral radius is 0.9992694 estimated iterations to convergence 292 setup time was (sec) 1.210000 now iterating at: 14:40:19 rms-change max change #iterations 10.26078 444.0288 at 10iterations 6.013226 155.0869 at 20iterations 3.515605 84.81444 at 30iterations 2.049471 41.79233 at 40iterations 1.189350 21.86923 at 50iterations 0.6923956 13.44577 at 60iterations 0.4000022 8.229006 at 70iterations 0.2327416 4.302479 at 80iterations 0.1344734 2.606544 at 90iterations 7.7504113E-02 1.369934 at 100iterations 4.4930648E-02 0.8514390 at 110iterations 2.5915474E-02 0.4358597 at 120iterations 1.4982985E-02 0.2793082 at 130iterations 8.6433347E-03 0.1619143 at 140iterations 5.0001075E-03 9.7589493E-02 at 150iterations 2.8816320E-03 5.0498366E-02 at 160iterations 1.6677105E-03 3.0046940E-02 at 170iterations 9.6198497E-04 1.6759396E-02 at 180iterations finished qdiffx linear iterations at : 14:40:30 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 9.6198497E-04 1.6759396E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 14:40:31 12.552u 0.201s 0:13.06 97.6% 0+0k 0+0io 0pf+0w