Mon Oct 10 12:11:44 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 Mon Oct 10 2011 at 12:11:44 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7409103 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): 9.031000 57.08000 ymin,ymax (A): -8.741000 36.93200 zmin,zma (A): -2.931000 44.40800 x,y,z range (A): 48.04900 45.67300 47.33900 scale (grids/A): 0.7409103 object centre (A): 33.05550 14.09550 20.73850 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.46014 90.36691 89.76388 assigned negative charge : -323.3720 centred at (gu) : 89.46261 90.46159 89.96737 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8065 nv = 96 ne = 84 npr = 43257 no. pairs analyzed = 43257 no. exposed pairs = 2688 no. arc points = 19198 no. surface atoms = 901 nbur = 1216 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 613 mr = 4543 m= 8 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.2600000 number of dielectric boundary points 4003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1552 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8499 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0085453E-07 -3.1532869E-07 midg,1,midg; midg,igrid,midg -1.3968094E-08 -2.2754736E-07 1,midg,midg; igrid,midg,midg -1.2127309E-07 -1.0455778E-07 gauss-seidel spectral radius is 0.9905093 estimated iterations to convergence 83 setup time was (sec) 0.4900000 now iterating at: 12:11:45 rms-change max change #iterations 0.2462657 33.32901 at 10iterations 3.3958808E-02 4.146088 at 20iterations 4.5652720E-03 0.5694932 at 30iterations 6.1132014E-04 8.1424713E-02 at 40iterations 8.4121915E-05 1.0459900E-02 at 50iterations finished qdiffx linear iterations at : 12:11:48 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 8.4121915E-05 1.0459900E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 12:11:48 3.327u 0.208s 0:03.85 91.4% 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 Mon Oct 10 2011 at 12:11:48 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.222731 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): 9.031000 57.08000 ymin,ymax (A): -8.741000 36.93200 zmin,zma (A): -2.931000 44.40800 x,y,z range (A): 48.04900 45.67300 47.33900 scale (grids/A): 2.222731 object centre (A): 33.05550 14.09550 20.73850 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.38056 91.10065 89.29141 assigned negative charge : -323.3720 centred at (gu) : 88.38793 91.38483 89.90217 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 84272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19198 grid for indexing accessible points = 1.400000 m= 35081 mr = 58173 m= 8205 mr = 27063 m= 967 mr = 5937 m= 34 mr = 545 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2394 time to turn everything in is 0.6300000 number of dielectric boundary points 36834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15738 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) : 0.7409103 object centre at (A) : 33.05550 14.09550 20.73850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3231855E-02 -0.1284456 midg,1,midg; midg,igrid,midg -2.8557923E-02 -5.0455134E-02 1,midg,midg; igrid,midg,midg -1.1573917E-03 8.6579397E-03 gauss-seidel spectral radius is 0.9989297 estimated iterations to convergence 242 setup time was (sec) 0.9100000 now iterating at: 12:11:49 rms-change max change #iterations 5.147027 263.3614 at 10iterations 2.609145 80.81476 at 20iterations 1.330000 37.34726 at 30iterations 0.6800182 18.68676 at 40iterations 0.3477794 10.03693 at 50iterations 0.1771657 5.339983 at 60iterations 9.0496272E-02 2.686748 at 70iterations 4.6343978E-02 1.307566 at 80iterations 2.3605403E-02 0.7620125 at 90iterations 1.2072573E-02 0.3671465 at 100iterations 6.1774799E-03 0.1731558 at 110iterations 3.1422530E-03 8.7905884E-02 at 120iterations finished qdiffx linear iterations at : 12:11:56 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 3.1422530E-03 8.7905884E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 12:11:57 7.741u 0.237s 0:08.47 94.0% 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 Mon Oct 10 2011 at 12:11:57 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.334096 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): 9.031000 57.08000 ymin,ymax (A): -8.741000 36.93200 zmin,zma (A): -2.931000 44.40800 x,y,z range (A): 48.04900 45.67300 47.33900 scale (grids/A): 3.334096 object centre (A): 33.05550 14.09550 20.73850 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.57072 91.65109 88.93712 assigned negative charge : -323.3720 centred at (gu) : 87.58197 92.07721 89.85317 start vw surface at 0.1400000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 193947 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19198 grid for indexing accessible points = 1.400000 m= 105605 mr = 140237 m= 47612 mr = 87960 m= 15975 mr = 40134 m= 3893 mr = 13067 m= 607 mr = 3006 m= 40 mr = 396 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 7681 time to turn everything in is 1.980000 number of dielectric boundary points 82868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 15824 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) : 2.222731 object centre at (A) : 33.05550 14.09550 20.73850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1233920 -1.313594 midg,1,midg; midg,igrid,midg -0.2443635 -0.2901626 1,midg,midg; igrid,midg,midg -3.2331821E-02 4.6587046E-02 gauss-seidel spectral radius is 0.9993181 estimated iterations to convergence 302 setup time was (sec) 2.300000 now iterating at: 12:11:59 rms-change max change #iterations 11.02369 318.8614 at 10iterations 6.491679 132.9498 at 20iterations 3.832209 90.88481 at 30iterations 2.254961 43.29216 at 40iterations 1.324789 22.48978 at 50iterations 0.7797813 12.96446 at 60iterations 0.4585692 7.678475 at 70iterations 0.2695678 4.190331 at 80iterations 0.1577726 2.567660 at 90iterations 9.2957005E-02 1.500278 at 100iterations 5.4473978E-02 0.8557081 at 110iterations 3.2035436E-02 0.5766296 at 120iterations 1.8854314E-02 0.2922325 at 130iterations 1.1069216E-02 0.1871772 at 140iterations 6.4916476E-03 0.1115513 at 150iterations 3.8155878E-03 6.0898781E-02 at 160iterations 2.2361428E-03 3.4714699E-02 at 170iterations 1.3152651E-03 2.0442247E-02 at 180iterations finished qdiffx linear iterations at : 12:12:12 total time elapsed so far: 14.61000 # loops : 180 mean,max change (kT/e) : 1.3152651E-03 2.0442247E-02 energy calculations done at 14.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.79000 DelPhi exited at 12:12:12 14.790u 0.241s 0:15.56 96.5% 0+0k 0+0io 0pf+0w