Sat Oct 15 14:43:01 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 Sat Oct 15 2011 at 14:43:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5420467 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): -34.66900 31.00800 ymin,ymax (A): -21.08200 25.61900 zmin,zma (A): -40.46300 7.504000 x,y,z range (A): 65.67700 46.70100 47.96700 scale (grids/A): 0.5420467 object centre (A): -1.830502 2.268499 -16.47950 number of atom coordinates read : 2959 total number of charged atoms : 2818 net assigned charge : -4.499968 assigned positive charge : 441.7610 centred at (gu) : 89.40327 90.17950 90.50956 assigned negative charge : -446.2621 centred at (gu) : 89.32384 90.04264 90.57104 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5565 nv = 96 ne = 84 npr = 59443 no. pairs analyzed = 59443 no. exposed pairs = 3913 no. arc points = 27393 no. surface atoms = 1324 nbur = 1635 mkacc time = 0.1100000 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= 216 mr = 2743 m= 3 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2799 ## 394 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7425 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0016517E-10 -6.7229716E-10 midg,1,midg; midg,igrid,midg -9.9101416E-10 5.6375227E-10 1,midg,midg; igrid,midg,midg -8.0941792E-10 1.8496052E-10 gauss-seidel spectral radius is 0.9824573 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 14:43:02 rms-change max change #iterations 6.9921255E-02 11.15863 at 10iterations 4.5378623E-03 0.7115228 at 20iterations 2.9387226E-04 6.5639496E-02 at 30iterations 1.9147556E-05 3.3779144E-03 at 40iterations 1.2378052E-06 1.9073486E-04 at 50iterations finished qdiffx linear iterations at : 14:43:07 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.2378052E-06 1.9073486E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 14:43:08 3.566u 0.204s 0:06.78 55.4% 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 Sat Oct 15 2011 at 14:43:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.626140 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): -34.66900 31.00800 ymin,ymax (A): -21.08200 25.61900 zmin,zma (A): -40.46300 7.504000 x,y,z range (A): 65.67700 46.70100 47.96700 scale (grids/A): 1.626140 object centre (A): -1.830502 2.268499 -16.47950 number of atom coordinates read : 2959 total number of charged atoms : 2818 net assigned charge : -4.499968 assigned positive charge : 441.7610 centred at (gu) : 88.20895 90.53809 91.52831 assigned negative charge : -446.2621 centred at (gu) : 87.97109 90.12769 91.71272 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27393 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18058 mr = 41174 m= 1721 mr = 11893 m= 33 mr = 726 m= 0 mr = 3 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 849 time to turn everything in is 0.3000000 number of dielectric boundary points 28281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 333 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 21604 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) : 0.5420467 object centre at (A) : -1.830502 2.268499 -16.47950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9821952E-04 -4.4385996E-03 midg,1,midg; midg,igrid,midg -1.4890780E-02 7.0676710E-03 1,midg,midg; igrid,midg,midg -2.1085557E-02 -3.0897351E-03 gauss-seidel spectral radius is 0.9981673 estimated iterations to convergence 186 setup time was (sec) 0.5300000 now iterating at: 14:43:09 rms-change max change #iterations 3.270545 145.6091 at 10iterations 1.354672 58.17217 at 20iterations 0.5608147 22.76246 at 30iterations 0.2332346 9.729257 at 40iterations 9.6353307E-02 3.780538 at 50iterations 3.9875947E-02 1.430573 at 60iterations 1.6553929E-02 0.5787086 at 70iterations 6.8877097E-03 0.2748108 at 80iterations 2.8536085E-03 0.1173401 at 90iterations 1.1853392E-03 4.3273926E-02 at 100iterations 4.9195660E-04 1.7921403E-02 at 110iterations 2.0461704E-04 8.3665848E-03 at 120iterations finished qdiffx linear iterations at : 14:43:20 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 2.0461704E-04 8.3665848E-03 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 14:43:21 8.215u 0.259s 0:13.00 65.0% 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 Sat Oct 15 2011 at 14:43:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.439210 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): -34.66900 31.00800 ymin,ymax (A): -21.08200 25.61900 zmin,zma (A): -40.46300 7.504000 x,y,z range (A): 65.67700 46.70100 47.96700 scale (grids/A): 2.439210 object centre (A): -1.830502 2.268499 -16.47950 number of atom coordinates read : 2959 total number of charged atoms : 2818 net assigned charge : -4.499968 assigned positive charge : 441.7610 centred at (gu) : 87.31339 90.80676 92.29218 assigned negative charge : -446.2621 centred at (gu) : 86.95657 90.19132 92.56892 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 144740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27393 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63337 mr = 100955 m= 17019 mr = 49086 m= 2493 mr = 12274 m= 136 mr = 1500 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 2719 time to turn everything in is 0.7500000 number of dielectric boundary points 63854 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 22514 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) : 1.626140 object centre at (A) : -1.830502 2.268499 -16.47950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6697544E-02 -4.5154225E-02 midg,1,midg; midg,igrid,midg -0.1999085 0.1189289 1,midg,midg; igrid,midg,midg -0.5401308 2.9386949E-02 gauss-seidel spectral radius is 0.9991374 estimated iterations to convergence 269 setup time was (sec) 1.010000 now iterating at: 14:43:23 rms-change max change #iterations 8.573157 283.5176 at 10iterations 4.791771 109.6630 at 20iterations 2.669296 63.74088 at 30iterations 1.480139 39.63929 at 40iterations 0.8170952 18.77273 at 50iterations 0.4519457 10.06849 at 60iterations 0.2487665 5.247935 at 70iterations 0.1374350 3.137659 at 80iterations 7.5439706E-02 1.479353 at 90iterations 4.1373760E-02 0.8427830 at 100iterations 2.2694860E-02 0.4803810 at 110iterations 1.2471380E-02 0.2647057 at 120iterations 6.8481676E-03 0.1562328 at 130iterations 3.7601269E-03 9.4306946E-02 at 140iterations 2.0582322E-03 4.5982361E-02 at 150iterations 1.1311631E-03 3.0197144E-02 at 160iterations 6.1901589E-04 1.2667656E-02 at 170iterations 3.4045335E-04 7.2174072E-03 at 180iterations finished qdiffx linear iterations at : 14:43:42 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 3.4045335E-04 7.2174072E-03 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 14:43:43 12.999u 0.237s 0:21.79 60.6% 0+0k 0+0io 0pf+0w