Mon Oct 10 09:22:02 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 09:22:02 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 !!! WARNING: HIT 233 has a net charge of 0.5140 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: 0.5883422 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): -17.82100 33.68100 ymin,ymax (A): -59.78500 -0.2600000 zmin,zma (A): -0.9030000 59.60600 x,y,z range (A): 51.50200 59.52500 60.50900 scale (grids/A): 0.5883422 object centre (A): 7.930000 -30.02250 29.35150 number of atom coordinates read : 2867 total number of charged atoms : 2717 net assigned charge : 9.014020 assigned positive charge : 422.2618 centred at (gu) : 88.16615 88.46143 87.99594 assigned negative charge : -413.2483 centred at (gu) : 88.26123 88.24736 87.86803 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6762 nv = 96 ne = 84 npr = 54656 no. pairs analyzed = 54656 no. exposed pairs = 4449 no. arc points = 31932 no. surface atoms = 1470 nbur = 1397 mkacc time = 0.1000000 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 = 1.484000 m= 364 mr = 2930 m= 2 mr = 18 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 0.2100000 number of dielectric boundary points 4180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3115 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8383 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2620084E-09 3.8475405E-09 midg,1,midg; midg,igrid,midg -4.5398187E-09 5.8083756E-09 1,midg,midg; igrid,midg,midg 7.9884002E-09 1.5034977E-10 gauss-seidel spectral radius is 0.9850982 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 09:22:03 rms-change max change #iterations 0.1011597 16.09244 at 10iterations 7.9375664E-03 1.212605 at 20iterations 6.5303303E-04 9.9145889E-02 at 30iterations 5.6659850E-05 8.1501007E-03 at 40iterations 6.9235880E-06 9.7250938E-04 at 50iterations finished qdiffx linear iterations at : 09:22:06 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 6.9235880E-06 9.7250938E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 09:22:06 3.406u 0.187s 0:03.97 90.1% 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 09:22:06 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 !!! WARNING: HIT 233 has a net charge of 0.5140 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: 1.765027 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): -17.82100 33.68100 ymin,ymax (A): -59.78500 -0.2600000 zmin,zma (A): -0.9030000 59.60600 x,y,z range (A): 51.50200 59.52500 60.50900 scale (grids/A): 1.765027 object centre (A): 7.930000 -30.02250 29.35150 number of atom coordinates read : 2867 total number of charged atoms : 2717 net assigned charge : 9.014020 assigned positive charge : 422.2618 centred at (gu) : 84.49821 85.38380 83.98740 assigned negative charge : -413.2483 centred at (gu) : 84.78318 84.74186 83.60371 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31932 grid for indexing accessible points = 1.400000 m= 23071 mr = 43845 m= 2993 mr = 14473 m= 136 mr = 1350 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 38780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 21114 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) : 0.5883422 object centre at (A) : 7.930000 -30.02250 29.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2910115E-02 1.2078987E-02 midg,1,midg; midg,igrid,midg 2.0831600E-02 4.2012405E-02 1,midg,midg; igrid,midg,midg 1.2927228E-02 8.1508532E-03 gauss-seidel spectral radius is 0.9984651 estimated iterations to convergence 202 setup time was (sec) 0.5900000 now iterating at: 09:22:07 rms-change max change #iterations 3.775720 172.4242 at 10iterations 1.682301 57.74209 at 20iterations 0.7497999 26.70307 at 30iterations 0.3332833 11.97709 at 40iterations 0.1483719 4.934152 at 50iterations 6.6188551E-02 2.581322 at 60iterations 2.9522268E-02 1.012480 at 70iterations 1.3175411E-02 0.4716606 at 80iterations 5.8794362E-03 0.1884594 at 90iterations 2.6314778E-03 9.7469330E-02 at 100iterations 1.1760730E-03 4.2663574E-02 at 110iterations 5.2555843E-04 1.8212795E-02 at 120iterations finished qdiffx linear iterations at : 09:22:14 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 5.2555843E-04 1.8212795E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 09:22:15 7.865u 0.199s 0:08.33 96.6% 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 09:22:15 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 !!! WARNING: HIT 233 has a net charge of 0.5140 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: 2.647540 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): -17.82100 33.68100 ymin,ymax (A): -59.78500 -0.2600000 zmin,zma (A): -0.9030000 59.60600 x,y,z range (A): 51.50200 59.52500 60.50900 scale (grids/A): 2.647540 object centre (A): 7.930000 -30.02250 29.35150 number of atom coordinates read : 2867 total number of charged atoms : 2717 net assigned charge : 9.014020 assigned positive charge : 422.2618 centred at (gu) : 81.74703 83.07550 80.98114 assigned negative charge : -413.2483 centred at (gu) : 82.17476 82.11276 80.40543 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 166602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31932 grid for indexing accessible points = 1.400000 m= 75382 mr = 108105 m= 24493 mr = 55856 m= 4928 mr = 17220 m= 484 mr = 2950 m= 23 mr = 191 m= 0 mr = 3 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 87587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 21727 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) : 1.765027 object centre at (A) : 7.930000 -30.02250 29.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7991720E-03 8.8898435E-02 midg,1,midg; midg,igrid,midg 0.4858563 0.4845550 1,midg,midg; igrid,midg,midg 7.0592187E-02 0.1200778 gauss-seidel spectral radius is 0.9992429 estimated iterations to convergence 287 setup time was (sec) 1.160000 now iterating at: 09:22:16 rms-change max change #iterations 9.679655 320.1111 at 10iterations 5.800304 147.8272 at 20iterations 3.405687 79.11362 at 30iterations 1.989509 56.74386 at 40iterations 1.157249 26.78169 at 50iterations 0.6701378 15.71417 at 60iterations 0.3870455 8.985551 at 70iterations 0.2227991 4.862426 at 80iterations 0.1282098 2.673522 at 90iterations 7.3568620E-02 1.493943 at 100iterations 4.2162176E-02 0.8834839 at 110iterations 2.4209211E-02 0.5275307 at 120iterations 1.3822419E-02 0.2833979 at 130iterations 7.9155006E-03 0.1552086 at 140iterations 4.5209653E-03 9.4474792E-02 at 150iterations 2.5857373E-03 5.1189423E-02 at 160iterations 1.4772776E-03 2.7890921E-02 at 170iterations 8.4367575E-04 1.5888214E-02 at 180iterations finished qdiffx linear iterations at : 09:22:28 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 8.4367575E-04 1.5888214E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 09:22:28 12.872u 0.204s 0:13.35 97.9% 0+0k 0+0io 0pf+0w