Sun Oct 9 14:13:20 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 Sun Oct 9 2011 at 14:13:20 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 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: 0.5691447 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): -7.0999980E-02 52.45300 ymin,ymax (A): -9.783999 38.66600 zmin,zma (A): -15.67100 46.87900 x,y,z range (A): 52.52400 48.45000 62.55000 scale (grids/A): 0.5691447 object centre (A): 26.19100 14.44100 15.60400 number of atom coordinates read : 2693 total number of charged atoms : 2552 net assigned charge : 8.539021 assigned positive charge : 411.2625 centred at (gu) : 89.64787 90.87778 88.54880 assigned negative charge : -402.7245 centred at (gu) : 89.60606 90.71571 88.62699 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5762 nv = 96 ne = 84 npr = 52856 no. pairs analyzed = 52856 no. exposed pairs = 3509 no. arc points = 24979 no. surface atoms = 1171 nbur = 1522 mkacc time = 8.9999996E-02 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= 253 mr = 2901 m= 0 mr = 8 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2565 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7318 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2484211E-09 1.1603868E-10 midg,1,midg; midg,igrid,midg -8.3692620E-10 4.2226129E-09 1,midg,midg; igrid,midg,midg 7.0437606E-10 1.6622055E-09 gauss-seidel spectral radius is 0.9840512 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 14:13:21 rms-change max change #iterations 8.5934222E-02 15.76197 at 10iterations 6.4811907E-03 1.012247 at 20iterations 4.7895679E-04 7.4626923E-02 at 30iterations 3.5818382E-05 5.2881241E-03 at 40iterations 2.6693067E-06 4.5013428E-04 at 50iterations finished qdiffx linear iterations at : 14:13:24 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.6693067E-06 4.5013428E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 14:13:24 3.424u 0.175s 0:03.86 93.0% 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 Sun Oct 9 2011 at 14:13:24 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 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: 1.707434 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): -7.0999980E-02 52.45300 ymin,ymax (A): -9.783999 38.66600 zmin,zma (A): -15.67100 46.87900 x,y,z range (A): 52.52400 48.45000 62.55000 scale (grids/A): 1.707434 object centre (A): 26.19100 14.44100 15.60400 number of atom coordinates read : 2693 total number of charged atoms : 2552 net assigned charge : 8.539021 assigned positive charge : 411.2625 centred at (gu) : 88.94305 92.63291 85.64600 assigned negative charge : -402.7245 centred at (gu) : 88.81783 92.14702 85.88078 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24979 grid for indexing accessible points = 1.400000 m= 19963 mr = 41659 m= 2237 mr = 13524 m= 87 mr = 1088 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 28780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19724 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) : 0.5691447 object centre at (A) : 26.19100 14.44100 15.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9852948E-02 8.5168611E-03 midg,1,midg; midg,igrid,midg 1.6366139E-04 1.5668932E-02 1,midg,midg; igrid,midg,midg -1.1437806E-02 -2.4995273E-03 gauss-seidel spectral radius is 0.9983246 estimated iterations to convergence 194 setup time was (sec) 0.5300000 now iterating at: 14:13:25 rms-change max change #iterations 3.456081 161.0435 at 10iterations 1.486014 57.59554 at 20iterations 0.6434662 24.87011 at 30iterations 0.2773233 10.31857 at 40iterations 0.1193703 4.110069 at 50iterations 5.1403925E-02 2.007805 at 60iterations 2.2141686E-02 0.9142852 at 70iterations 9.5738238E-03 0.3227463 at 80iterations 4.1386806E-03 0.1383450 at 90iterations 1.7823445E-03 6.6431046E-02 at 100iterations 7.6800422E-04 2.5451660E-02 at 110iterations 3.3285283E-04 1.2153625E-02 at 120iterations finished qdiffx linear iterations at : 14:13:32 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 3.3285283E-04 1.2153625E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 14:13:32 7.733u 0.195s 0:08.25 96.0% 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 Sun Oct 9 2011 at 14:13:32 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 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: 2.561151 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): -7.0999980E-02 52.45300 ymin,ymax (A): -9.783999 38.66600 zmin,zma (A): -15.67100 46.87900 x,y,z range (A): 52.52400 48.45000 62.55000 scale (grids/A): 2.561151 object centre (A): 26.19100 14.44100 15.60400 number of atom coordinates read : 2693 total number of charged atoms : 2552 net assigned charge : 8.539021 assigned positive charge : 411.2625 centred at (gu) : 88.41444 93.94932 83.46877 assigned negative charge : -402.7245 centred at (gu) : 88.22669 93.22026 83.82109 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 145412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24979 grid for indexing accessible points = 1.400000 m= 67485 mr = 101763 m= 20140 mr = 52872 m= 3539 mr = 14917 m= 312 mr = 2232 m= 16 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 64967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20396 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) : 1.707434 object centre at (A) : 26.19100 14.44100 15.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.083313 0.1329266 midg,1,midg; midg,igrid,midg -2.0349350E-02 0.1489510 1,midg,midg; igrid,midg,midg -0.1451562 -6.5570652E-02 gauss-seidel spectral radius is 0.9991771 estimated iterations to convergence 275 setup time was (sec) 1.010000 now iterating at: 14:13:34 rms-change max change #iterations 8.857238 293.6017 at 10iterations 5.124207 134.6653 at 20iterations 2.935896 75.64891 at 30iterations 1.662440 38.39865 at 40iterations 0.9423980 24.41841 at 50iterations 0.5318298 12.78799 at 60iterations 0.2991514 6.397124 at 70iterations 0.1677743 3.896545 at 80iterations 9.4324857E-02 2.089765 at 90iterations 5.2856669E-02 1.192354 at 100iterations 2.9511780E-02 0.6107597 at 110iterations 1.6492253E-02 0.3577137 at 120iterations 9.2228213E-03 0.1797361 at 130iterations 5.1382328E-03 0.1114216 at 140iterations 2.8747492E-03 6.3541412E-02 at 150iterations 1.6018936E-03 3.7811756E-02 at 160iterations 8.9384406E-04 2.1766663E-02 at 170iterations 4.9857178E-04 1.1435509E-02 at 180iterations finished qdiffx linear iterations at : 14:13:46 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 4.9857178E-04 1.1435509E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 14:13:47 13.567u 0.204s 0:14.11 97.5% 0+0k 0+0io 0pf+0w