Sat Oct 15 15:22:55 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 Sat Oct 15 2011 at 15:22:55 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3348 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5424845 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): 113.3730 170.7110 ymin,ymax (A): 18.16000 66.12000 zmin,zma (A): -11.11100 54.51300 x,y,z range (A): 57.33800 47.96000 65.62400 scale (grids/A): 0.5424845 object centre (A): 142.0420 42.14000 21.70100 number of atom coordinates read : 3348 total number of charged atoms : 3184 net assigned charge : 0.4510227 assigned positive charge : 512.5328 centred at (gu) : 90.23803 90.01434 88.41714 assigned negative charge : -512.0826 centred at (gu) : 90.38509 90.15437 88.29692 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6235 nv = 96 ne = 84 npr = 67726 no. pairs analyzed = 67726 no. exposed pairs = 4046 no. arc points = 28934 no. surface atoms = 1364 nbur = 1984 mkacc time = 0.1800000 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 = 1.568000 m= 227 mr = 3248 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2945 ## 422 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8251 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1599515E-09 5.6218968E-10 midg,1,midg; midg,igrid,midg 9.6026842E-10 -9.1320518E-10 1,midg,midg; igrid,midg,midg 9.5031882E-10 -1.0185400E-09 gauss-seidel spectral radius is 0.9825082 estimated iterations to convergence 62 setup time was (sec) 0.7100000 now iterating at: 15:22:56 rms-change max change #iterations 7.7335820E-02 14.37656 at 10iterations 5.1092696E-03 0.8041687 at 20iterations 3.4141171E-04 5.4357529E-02 at 30iterations 2.6187075E-05 4.8828125E-03 at 40iterations 3.9128267E-06 7.4958801E-04 at 50iterations finished qdiffx linear iterations at : 15:23:01 total time elapsed so far: 5.280000 # loops : 50 mean,max change (kT/e) : 3.9128267E-06 7.4958801E-04 energy calculations done at 5.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.430000 DelPhi exited at 15:23:01 5.437u 0.447s 0:06.14 95.6% 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 Sat Oct 15 2011 at 15:23:01 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3348 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.627453 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): 113.3730 170.7110 ymin,ymax (A): 18.16000 66.12000 zmin,zma (A): -11.11100 54.51300 x,y,z range (A): 57.33800 47.96000 65.62400 scale (grids/A): 1.627453 object centre (A): 142.0420 42.14000 21.70100 number of atom coordinates read : 3348 total number of charged atoms : 3184 net assigned charge : 0.4510227 assigned positive charge : 512.5328 centred at (gu) : 90.71358 90.04224 85.25063 assigned negative charge : -512.0826 centred at (gu) : 91.15475 90.46243 84.89037 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68166 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28934 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21846 mr = 45877 m= 2271 mr = 15349 m= 64 mr = 1076 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1736 time to turn everything in is 0.5800000 number of dielectric boundary points 30045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 396 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 24368 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) : 0.5424845 object centre at (A) : 142.0420 42.14000 21.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0875636E-02 7.4168723E-03 midg,1,midg; midg,igrid,midg 4.2528911E-03 -5.2713226E-03 1,midg,midg; igrid,midg,midg 2.1503238E-02 3.2681526E-04 gauss-seidel spectral radius is 0.9982069 estimated iterations to convergence 188 setup time was (sec) 0.9700000 now iterating at: 15:23:02 rms-change max change #iterations 3.577031 165.1580 at 10iterations 1.493403 60.19553 at 20iterations 0.6264439 21.08641 at 30iterations 0.2632094 9.842087 at 40iterations 0.1103103 3.969795 at 50iterations 4.6199363E-02 1.593607 at 60iterations 1.9396082E-02 0.6819363 at 70iterations 8.1190215E-03 0.3148232 at 80iterations 3.4106593E-03 0.1123199 at 90iterations 1.4283918E-03 5.2074432E-02 at 100iterations 6.0183479E-04 2.0675540E-02 at 110iterations 2.5316371E-04 9.1552734E-03 at 120iterations finished qdiffx linear iterations at : 15:23:14 total time elapsed so far: 12.44000 # loops : 120 mean,max change (kT/e) : 2.5316371E-04 9.1552734E-03 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 15:23:14 12.612u 0.521s 0:13.46 97.5% 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 Sat Oct 15 2011 at 15:23:15 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3348 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.441180 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): 113.3730 170.7110 ymin,ymax (A): 18.16000 66.12000 zmin,zma (A): -11.11100 54.51300 x,y,z range (A): 57.33800 47.96000 65.62400 scale (grids/A): 2.441180 object centre (A): 142.0420 42.14000 21.70100 number of atom coordinates read : 3348 total number of charged atoms : 3184 net assigned charge : 0.4510227 assigned positive charge : 512.5328 centred at (gu) : 91.06991 90.06309 82.87585 assigned negative charge : -512.0826 centred at (gu) : 91.73193 90.69361 82.33533 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 158485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28934 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 74731 mr = 112766 m= 22064 mr = 59414 m= 3526 mr = 16810 m= 222 mr = 2232 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 5870 time to turn everything in is 1.420000 number of dielectric boundary points 67723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 25434 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) : 1.627453 object centre at (A) : 142.0420 42.14000 21.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4506772E-02 8.8153534E-02 midg,1,midg; midg,igrid,midg 5.1894117E-02 -3.7074134E-02 1,midg,midg; igrid,midg,midg 0.2839082 5.6616198E-02 gauss-seidel spectral radius is 0.9991516 estimated iterations to convergence 271 setup time was (sec) 1.800000 now iterating at: 15:23:17 rms-change max change #iterations 9.154049 277.0792 at 10iterations 5.135315 121.3973 at 20iterations 2.867461 82.12038 at 30iterations 1.598230 33.78217 at 40iterations 0.8854896 19.00366 at 50iterations 0.4914682 9.726784 at 60iterations 0.2724462 5.307858 at 70iterations 0.1504856 3.051460 at 80iterations 8.3243079E-02 1.840144 at 90iterations 4.5862790E-02 0.9487190 at 100iterations 2.5307152E-02 0.5135298 at 110iterations 1.4006944E-02 0.2727623 at 120iterations 7.7416282E-03 0.1502190 at 130iterations 4.2728665E-03 8.5346222E-02 at 140iterations 2.3572440E-03 4.7122478E-02 at 150iterations 1.3014483E-03 2.8027058E-02 at 160iterations 7.1910664E-04 1.4679909E-02 at 170iterations 3.9787503E-04 7.8868866E-03 at 180iterations finished qdiffx linear iterations at : 15:23:36 total time elapsed so far: 21.01000 # loops : 180 mean,max change (kT/e) : 3.9787503E-04 7.8868866E-03 energy calculations done at 21.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.18000 DelPhi exited at 15:23:37 21.181u 0.556s 0:22.01 98.7% 0+0k 0+0io 0pf+0w