Tue Oct 11 08:20:50 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 08:20:50 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6977246 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): -28.92200 15.91400 ymin,ymax (A): -34.30100 12.09100 zmin,zma (A): 1.554000 52.57700 x,y,z range (A): 44.83600 46.39200 51.02300 scale (grids/A): 0.6977246 object centre (A): -6.504001 -11.10500 27.06550 number of atom coordinates read : 2105 total number of charged atoms : 1994 net assigned charge : 2.000009 assigned positive charge : 313.8145 centred at (gu) : 89.27219 89.51666 89.46113 assigned negative charge : -311.8150 centred at (gu) : 89.23904 89.47775 89.20627 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7069 nv = 96 ne = 84 npr = 42951 no. pairs analyzed = 42951 no. exposed pairs = 2731 no. arc points = 18989 no. surface atoms = 920 nbur = 1185 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 3911 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1683 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7933 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9770290E-08 1.0123420E-07 midg,1,midg; midg,igrid,midg -1.3780228E-09 2.6985994E-08 1,midg,midg; igrid,midg,midg 1.1785304E-09 2.3765088E-08 gauss-seidel spectral radius is 0.9893054 estimated iterations to convergence 79 setup time was (sec) 0.4700000 now iterating at: 08:20:51 rms-change max change #iterations 0.1935911 27.96152 at 10iterations 2.3046901E-02 3.328387 at 20iterations 2.7883784E-03 0.4277382 at 30iterations 3.6261891E-04 5.3783417E-02 at 40iterations 5.7738878E-05 9.6244812E-03 at 50iterations finished qdiffx linear iterations at : 08:20:53 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 5.7738878E-05 9.6244812E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 08:20:54 3.073u 0.151s 0:03.55 90.7% 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 08:20:54 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.093174 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): -28.92200 15.91400 ymin,ymax (A): -34.30100 12.09100 zmin,zma (A): 1.554000 52.57700 x,y,z range (A): 44.83600 46.39200 51.02300 scale (grids/A): 2.093174 object centre (A): -6.504001 -11.10500 27.06550 number of atom coordinates read : 2105 total number of charged atoms : 1994 net assigned charge : 2.000009 assigned positive charge : 313.8145 centred at (gu) : 87.81618 88.54972 88.38307 assigned negative charge : -311.8150 centred at (gu) : 87.71729 88.43320 87.61868 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18989 grid for indexing accessible points = 1.400000 m= 28002 mr = 52590 m= 5117 mr = 20717 m= 413 mr = 3241 m= 13 mr = 160 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 32515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 15818 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) : 0.6977246 object centre at (A) : -6.504001 -11.10500 27.06550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0030853E-02 7.1009934E-02 midg,1,midg; midg,igrid,midg -3.9382435E-02 1.0403804E-02 1,midg,midg; igrid,midg,midg -1.3954726E-02 1.4309322E-02 gauss-seidel spectral radius is 0.9988152 estimated iterations to convergence 230 setup time was (sec) 0.8100000 now iterating at: 08:20:55 rms-change max change #iterations 4.571963 186.1404 at 10iterations 2.243319 71.01573 at 20iterations 1.114074 34.22310 at 30iterations 0.5509280 16.89695 at 40iterations 0.2707118 7.870823 at 50iterations 0.1345350 4.106652 at 60iterations 6.6275917E-02 1.860535 at 70iterations 3.2812390E-02 1.038249 at 80iterations 1.6207550E-02 0.4826612 at 90iterations 7.9811951E-03 0.2883606 at 100iterations 3.9526182E-03 0.1216202 at 110iterations 1.9530823E-03 6.7969322E-02 at 120iterations finished qdiffx linear iterations at : 08:21:01 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 1.9530823E-03 6.7969322E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 08:21:02 7.052u 0.159s 0:07.64 94.2% 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 Tue Oct 11 2011 at 08:21:02 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 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: 3.139760 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): -28.92200 15.91400 ymin,ymax (A): -34.30100 12.09100 zmin,zma (A): 1.554000 52.57700 x,y,z range (A): 44.83600 46.39200 51.02300 scale (grids/A): 3.139760 object centre (A): -6.504001 -11.10500 27.06550 number of atom coordinates read : 2105 total number of charged atoms : 1994 net assigned charge : 2.000009 assigned positive charge : 313.8145 centred at (gu) : 86.72416 87.82446 87.57456 assigned negative charge : -311.8150 centred at (gu) : 86.57586 87.64986 86.42800 start vw surface at 0.1300000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 175041 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18989 grid for indexing accessible points = 1.400000 m= 88598 mr = 127702 m= 34984 mr = 72372 m= 9629 mr = 28342 m= 1649 mr = 7170 m= 129 mr = 1101 m= 4 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 73304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 15952 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) : 2.093174 object centre at (A) : -6.504001 -11.10500 27.06550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7684691 0.7315993 midg,1,midg; midg,igrid,midg -0.3690398 0.1300755 1,midg,midg; igrid,midg,midg -0.1447929 0.1122937 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 1.950000 now iterating at: 08:21:04 rms-change max change #iterations 10.19904 522.4348 at 10iterations 6.019597 129.3745 at 20iterations 3.545394 76.26338 at 30iterations 2.088196 43.00867 at 40iterations 1.229149 21.97027 at 50iterations 0.7199593 13.52110 at 60iterations 0.4236490 7.318996 at 70iterations 0.2480299 4.504747 at 80iterations 0.1450105 2.662749 at 90iterations 8.4935941E-02 1.491913 at 100iterations 4.9687497E-02 0.9028339 at 110iterations 2.9112356E-02 0.5106392 at 120iterations 1.7054291E-02 0.3141899 at 130iterations 9.9595031E-03 0.1718369 at 140iterations 5.8165165E-03 0.1057258 at 150iterations 3.4118481E-03 5.9692383E-02 at 160iterations 1.9989694E-03 3.7841797E-02 at 170iterations 1.1713878E-03 1.9570351E-02 at 180iterations finished qdiffx linear iterations at : 08:21:16 total time elapsed so far: 13.70000 # loops : 180 mean,max change (kT/e) : 1.1713878E-03 1.9570351E-02 energy calculations done at 13.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 08:21:16 13.862u 0.170s 0:14.32 97.9% 0+0k 0+0io 0pf+0w