Tue Oct 11 08:07:40 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 08:07:40 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 0.5648821 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): -18.92100 25.52800 ymin,ymax (A): 16.84900 79.87100 zmin,zma (A): 2.529000 52.24700 x,y,z range (A): 44.44900 63.02200 49.71800 scale (grids/A): 0.5648821 object centre (A): 3.303500 48.36000 27.38800 number of atom coordinates read : 2382 total number of charged atoms : 2245 net assigned charge : 9.000023 assigned positive charge : 363.1702 centred at (gu) : 90.20380 88.60764 91.51730 assigned negative charge : -354.1708 centred at (gu) : 90.07852 88.70671 91.49825 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5044 nv = 96 ne = 84 npr = 47243 no. pairs analyzed = 47243 no. exposed pairs = 3107 no. arc points = 22167 no. surface atoms = 1037 nbur = 1345 mkacc time = 0.1400000 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 = 1.512000 m= 210 mr = 2569 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2264 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6426 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5165162E-10 1.8862079E-09 midg,1,midg; midg,igrid,midg 2.9909004E-09 6.5463517E-11 1,midg,midg; igrid,midg,midg -1.9559507E-10 2.5279867E-09 gauss-seidel spectral radius is 0.9837869 estimated iterations to convergence 65 setup time was (sec) 0.5800000 now iterating at: 08:07:41 rms-change max change #iterations 7.7417590E-02 14.27881 at 10iterations 5.7257032E-03 1.042397 at 20iterations 4.3641849E-04 7.0669174E-02 at 30iterations 5.5047243E-05 1.3842583E-02 at 40iterations 1.3663920E-05 3.7927628E-03 at 50iterations finished qdiffx linear iterations at : 08:07:44 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 1.3663920E-05 3.7927628E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 08:07:45 4.112u 0.308s 0:04.72 93.4% 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 08:07:45 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 1.694646 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): -18.92100 25.52800 ymin,ymax (A): 16.84900 79.87100 zmin,zma (A): 2.529000 52.24700 x,y,z range (A): 44.44900 63.02200 49.71800 scale (grids/A): 1.694646 object centre (A): 3.303500 48.36000 27.38800 number of atom coordinates read : 2382 total number of charged atoms : 2245 net assigned charge : 9.000023 assigned positive charge : 363.1702 centred at (gu) : 90.61105 85.82260 94.55122 assigned negative charge : -354.1708 centred at (gu) : 90.23547 86.11996 94.49461 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 55453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22167 grid for indexing accessible points = 1.400000 m= 17662 mr = 36946 m= 2002 mr = 12256 m= 61 mr = 1053 m= 0 mr = 6 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.5200000 number of dielectric boundary points 24917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17340 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) : 0.5648821 object centre at (A) : 3.303500 48.36000 27.38800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3062245E-04 1.4161609E-02 midg,1,midg; midg,igrid,midg 5.5884760E-02 2.4830146E-02 1,midg,midg; igrid,midg,midg -5.4064719E-03 1.1877705E-02 gauss-seidel spectral radius is 0.9982522 estimated iterations to convergence 190 setup time was (sec) 0.8300000 now iterating at: 08:07:46 rms-change max change #iterations 3.193531 158.7838 at 10iterations 1.339173 56.53643 at 20iterations 0.5672578 21.94067 at 30iterations 0.2403608 8.995037 at 40iterations 0.1015392 4.298004 at 50iterations 4.3245398E-02 1.834507 at 60iterations 1.8225633E-02 0.6963558 at 70iterations 7.7790949E-03 0.2938652 at 80iterations 3.3132425E-03 0.1384029 at 90iterations 1.4326802E-03 6.0344219E-02 at 100iterations 6.3637173E-04 2.6729584E-02 at 110iterations 2.9923150E-04 1.4453888E-02 at 120iterations finished qdiffx linear iterations at : 08:07:54 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 2.9923150E-04 1.4453888E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 08:07:55 9.356u 0.306s 0:09.96 96.8% 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 08:07:55 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 2.541969 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): -18.92100 25.52800 ymin,ymax (A): 16.84900 79.87100 zmin,zma (A): 2.529000 52.24700 x,y,z range (A): 44.44900 63.02200 49.71800 scale (grids/A): 2.541969 object centre (A): 3.303500 48.36000 27.38800 number of atom coordinates read : 2382 total number of charged atoms : 2245 net assigned charge : 9.000023 assigned positive charge : 363.1702 centred at (gu) : 90.91639 83.73377 96.82680 assigned negative charge : -354.1708 centred at (gu) : 90.35330 84.18006 96.74196 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 128440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22167 grid for indexing accessible points = 1.400000 m= 60126 mr = 90268 m= 17898 mr = 47559 m= 3156 mr = 13532 m= 276 mr = 2192 m= 3 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 188 time to turn everything in is 1.220000 number of dielectric boundary points 56201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 17943 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) : 1.694646 object centre at (A) : 3.303500 48.36000 27.38800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1588387E-04 0.1990122 midg,1,midg; midg,igrid,midg 0.8046406 0.4842849 1,midg,midg; igrid,midg,midg -6.5772638E-02 0.1516761 gauss-seidel spectral radius is 0.9991447 estimated iterations to convergence 270 setup time was (sec) 1.540000 now iterating at: 08:07:57 rms-change max change #iterations 8.164760 301.3990 at 10iterations 4.571780 123.2441 at 20iterations 2.558065 63.93514 at 30iterations 1.422616 40.97103 at 40iterations 0.7891375 20.22873 at 50iterations 0.4368978 10.45799 at 60iterations 0.2418597 6.048546 at 70iterations 0.1335663 2.948562 at 80iterations 7.3696375E-02 1.870300 at 90iterations 4.0703278E-02 0.9287109 at 100iterations 2.2464974E-02 0.4825597 at 110iterations 1.2361646E-02 0.2721424 at 120iterations 6.8284795E-03 0.1469064 at 130iterations 3.7667563E-03 8.6114883E-02 at 140iterations 2.0832806E-03 4.6062469E-02 at 150iterations 1.1585223E-03 2.8236389E-02 at 160iterations 6.5000454E-04 1.5090942E-02 at 170iterations 3.7241849E-04 9.9754333E-03 at 180iterations finished qdiffx linear iterations at : 08:08:11 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 3.7241849E-04 9.9754333E-03 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.58000 DelPhi exited at 08:08:11 15.584u 0.341s 0:16.40 97.0% 0+0k 0+0io 0pf+0w