Sun Oct 9 15:00:07 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 Sun Oct 9 2011 at 15:00:07 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 = 1138 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 0.7810444 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): -42.31500 -5.177000 ymin,ymax (A): 5.943000 39.01600 zmin,zma (A): -22.04700 23.53300 x,y,z range (A): 37.13800 33.07300 45.58000 scale (grids/A): 0.7810444 object centre (A): -23.74600 22.47950 0.7430000 number of atom coordinates read : 1138 total number of charged atoms : 1010 net assigned charge : 1.500005 assigned positive charge : 162.7672 centred at (gu) : 89.69824 88.97886 88.96810 assigned negative charge : -161.2671 centred at (gu) : 89.73401 88.78783 89.09764 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4872 nv = 96 ne = 84 npr = 23554 no. pairs analyzed = 23554 no. exposed pairs = 1464 no. arc points = 10447 no. surface atoms = 489 nbur = 649 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 2660 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.2200000 number of dielectric boundary points 2489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 734 ## 61 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 4587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4939305E-07 -7.0387863E-08 midg,1,midg; midg,igrid,midg -1.9077795E-07 2.2852430E-07 1,midg,midg; igrid,midg,midg 1.0824257E-07 2.0870470E-08 gauss-seidel spectral radius is 0.9913497 estimated iterations to convergence 87 setup time was (sec) 0.4300000 now iterating at: 15:00:08 rms-change max change #iterations 0.2106782 39.29048 at 10iterations 3.1144490E-02 5.119160 at 20iterations 4.5596552E-03 0.6861839 at 30iterations 6.8301923E-04 0.1144805 at 40iterations 9.9471719E-05 1.6805649E-02 at 50iterations finished qdiffx linear iterations at : 15:00:10 total time elapsed so far: 2.820000 # loops : 50 mean,max change (kT/e) : 9.9471719E-05 1.6805649E-02 energy calculations done at 2.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.990000 DelPhi exited at 15:00:11 2.998u 0.137s 0:03.45 90.4% 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 Sun Oct 9 2011 at 15:00:11 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 = 1138 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 2.343133 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): -42.31500 -5.177000 ymin,ymax (A): 5.943000 39.01600 zmin,zma (A): -22.04700 23.53300 x,y,z range (A): 37.13800 33.07300 45.58000 scale (grids/A): 2.343133 object centre (A): -23.74600 22.47950 0.7430000 number of atom coordinates read : 1138 total number of charged atoms : 1010 net assigned charge : 1.500005 assigned positive charge : 162.7672 centred at (gu) : 89.09501 86.93701 86.90458 assigned negative charge : -161.2671 centred at (gu) : 89.20214 86.36342 87.29294 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 50550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10447 grid for indexing accessible points = 1.400000 m= 20425 mr = 34037 m= 4455 mr = 15693 m= 459 mr = 3115 m= 22 mr = 244 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 4719 time to turn everything in is 0.3900000 number of dielectric boundary points 22820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8066 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) : 0.7810444 object centre at (A) : -23.74600 22.47950 0.7430000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0474006E-02 8.1179328E-03 midg,1,midg; midg,igrid,midg -1.8112382E-02 1.4667802E-02 1,midg,midg; igrid,midg,midg 2.1798130E-02 1.3954176E-02 gauss-seidel spectral radius is 0.9989261 estimated iterations to convergence 241 setup time was (sec) 0.6400000 now iterating at: 15:00:12 rms-change max change #iterations 3.825831 257.3246 at 10iterations 1.946904 102.8798 at 20iterations 0.9915663 36.87162 at 30iterations 0.5079708 18.52089 at 40iterations 0.2590848 9.692590 at 50iterations 0.1314611 4.723265 at 60iterations 6.7199178E-02 2.424294 at 70iterations 3.4111463E-02 1.146243 at 80iterations 1.7434450E-02 0.6354790 at 90iterations 8.8436333E-03 0.4023323 at 100iterations 4.5089796E-03 0.1684170 at 110iterations 2.2979651E-03 8.3522320E-02 at 120iterations finished qdiffx linear iterations at : 15:00:17 total time elapsed so far: 6.420000 # loops : 120 mean,max change (kT/e) : 2.2979651E-03 8.3522320E-02 energy calculations done at 6.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.600000 DelPhi exited at 15:00:18 6.601u 0.161s 0:07.03 96.1% 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 Sun Oct 9 2011 at 15:00:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1138 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 3.514700 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): -42.31500 -5.177000 ymin,ymax (A): 5.943000 39.01600 zmin,zma (A): -22.04700 23.53300 x,y,z range (A): 37.13800 33.07300 45.58000 scale (grids/A): 3.514700 object centre (A): -23.74600 22.47950 0.7430000 number of atom coordinates read : 1138 total number of charged atoms : 1010 net assigned charge : 1.500005 assigned positive charge : 162.7672 centred at (gu) : 88.64258 85.40562 85.35699 assigned negative charge : -161.2671 centred at (gu) : 88.80321 84.54519 85.93941 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 116123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10447 grid for indexing accessible points = 1.400000 m= 62188 mr = 81807 m= 27331 mr = 51798 m= 8613 mr = 22901 m= 1862 mr = 6907 m= 219 mr = 1401 m= 7 mr = 121 m= 0 mr = 3 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 15957 time to turn everything in is 1.190000 number of dielectric boundary points 51405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 8080 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) : 2.343133 object centre at (A) : -23.74600 22.47950 0.7430000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3608042E-02 0.1253700 midg,1,midg; midg,igrid,midg -0.1566223 8.2177147E-02 1,midg,midg; igrid,midg,midg 0.1477605 5.8871772E-02 gauss-seidel spectral radius is 0.9993057 estimated iterations to convergence 299 setup time was (sec) 1.450000 now iterating at: 15:00:20 rms-change max change #iterations 8.207294 273.3274 at 10iterations 4.799712 130.0677 at 20iterations 2.806983 63.95612 at 30iterations 1.643237 34.50877 at 40iterations 0.9599881 20.47192 at 50iterations 0.5608112 11.56888 at 60iterations 0.3278852 6.800415 at 70iterations 0.1914698 4.161307 at 80iterations 0.1118026 2.172644 at 90iterations 6.5192811E-02 1.346436 at 100iterations 3.8204364E-02 0.7682371 at 110iterations 2.2306792E-02 0.4471760 at 120iterations 1.3038078E-02 0.2485924 at 130iterations 7.5963764E-03 0.1412640 at 140iterations 4.4328938E-03 8.3302915E-02 at 150iterations 2.5935196E-03 4.8980713E-02 at 160iterations 1.5123825E-03 3.1299591E-02 at 170iterations 8.8391535E-04 1.7970562E-02 at 180iterations finished qdiffx linear iterations at : 15:00:29 total time elapsed so far: 10.78000 # loops : 180 mean,max change (kT/e) : 8.8391535E-04 1.7970562E-02 energy calculations done at 10.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.95000 DelPhi exited at 15:00:29 10.954u 0.174s 0:11.41 97.4% 0+0k 0+0io 0pf+0w