Tue Oct 11 03:26:17 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 Tue Oct 11 2011 at 03:26:17 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3097 !!! WARNING: GLM 313 has a net charge of -0.0940 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 476 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5294704 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): -12.37300 38.91800 ymin,ymax (A): -27.43900 25.62100 zmin,zma (A): -19.98600 47.25100 x,y,z range (A): 51.29100 53.06000 67.23700 scale (grids/A): 0.5294704 object centre (A): 13.27250 -0.9089994 13.63250 number of atom coordinates read : 3097 total number of charged atoms : 2952 net assigned charge : 2.434017 assigned positive charge : 462.3358 centred at (gu) : 89.63158 90.25776 90.91065 assigned negative charge : -459.9031 centred at (gu) : 89.64386 90.30570 90.94413 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5704 nv = 96 ne = 84 npr = 60744 no. pairs analyzed = 60744 no. exposed pairs = 4517 no. arc points = 32171 no. surface atoms = 1499 nbur = 1598 mkacc time = 0.1400000 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 = 1.596000 m= 213 mr = 2571 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3112 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5931016E-10 -5.5341929E-11 midg,1,midg; midg,igrid,midg 2.3655347E-10 -1.0285835E-10 1,midg,midg; igrid,midg,midg 1.3604350E-10 3.1872692E-11 gauss-seidel spectral radius is 0.9816439 estimated iterations to convergence 61 setup time was (sec) 0.5700000 now iterating at: 03:26:18 rms-change max change #iterations 6.5914422E-02 12.43414 at 10iterations 4.2289016E-03 0.7368965 at 20iterations 4.0313270E-04 6.5608978E-02 at 30iterations 6.6891735E-05 1.2058258E-02 at 40iterations 1.3354123E-05 2.3536682E-03 at 50iterations finished qdiffx linear iterations at : 03:26:21 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.3354123E-05 2.3536682E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 03:26:21 3.400u 0.186s 0:03.86 92.7% 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 Tue Oct 11 2011 at 03:26:21 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3097 !!! WARNING: GLM 313 has a net charge of -0.0940 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 476 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.588411 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): -12.37300 38.91800 ymin,ymax (A): -27.43900 25.62100 zmin,zma (A): -19.98600 47.25100 x,y,z range (A): 51.29100 53.06000 67.23700 scale (grids/A): 1.588411 object centre (A): 13.27250 -0.9089994 13.63250 number of atom coordinates read : 3097 total number of charged atoms : 2952 net assigned charge : 2.434017 assigned positive charge : 462.3358 centred at (gu) : 88.89429 90.77249 92.73108 assigned negative charge : -459.9031 centred at (gu) : 88.93101 90.91668 92.83199 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32171 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18189 mr = 39159 m= 1888 mr = 11537 m= 71 mr = 849 m= 3 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 31114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 343 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 22436 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) : 0.5294704 object centre at (A) : 13.27250 -0.9089994 13.63250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2968900E-03 -3.4346469E-04 midg,1,midg; midg,igrid,midg 5.7770167E-03 -3.1628076E-03 1,midg,midg; igrid,midg,midg 3.0325097E-03 8.4706647E-03 gauss-seidel spectral radius is 0.9981179 estimated iterations to convergence 183 setup time was (sec) 0.7700000 now iterating at: 03:26:22 rms-change max change #iterations 3.208613 150.5386 at 10iterations 1.304089 47.55571 at 20iterations 0.5323916 21.18089 at 30iterations 0.2184266 8.635592 at 40iterations 8.9276776E-02 3.123316 at 50iterations 3.6714949E-02 1.315109 at 60iterations 1.5055826E-02 0.5706487 at 70iterations 6.1947373E-03 0.2298946 at 80iterations 2.5492583E-03 0.1059189 at 90iterations 1.0544822E-03 4.2352676E-02 at 100iterations 4.4120109E-04 1.9886017E-02 at 110iterations 1.8741148E-04 7.7362061E-03 at 120iterations finished qdiffx linear iterations at : 03:26:29 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 1.8741148E-04 7.7362061E-03 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 03:26:29 7.532u 0.252s 0:08.11 95.9% 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 Tue Oct 11 2011 at 03:26:29 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3097 !!! WARNING: GLM 313 has a net charge of -0.0940 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 476 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.382617 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): -12.37300 38.91800 ymin,ymax (A): -27.43900 25.62100 zmin,zma (A): -19.98600 47.25100 x,y,z range (A): 51.29100 53.06000 67.23700 scale (grids/A): 2.382617 object centre (A): 13.27250 -0.9089994 13.63250 number of atom coordinates read : 3097 total number of charged atoms : 2952 net assigned charge : 2.434017 assigned positive charge : 462.3358 centred at (gu) : 88.34106 91.15842 94.09639 assigned negative charge : -459.9031 centred at (gu) : 88.39634 91.37505 94.24791 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 145113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32171 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 62555 mr = 97087 m= 17738 mr = 46674 m= 2876 mr = 12601 m= 190 mr = 1685 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.090000 number of dielectric boundary points 70370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 23593 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) : 1.588411 object centre at (A) : 13.27250 -0.9089994 13.63250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1181817 -1.0989554E-02 midg,1,midg; midg,igrid,midg 0.1075450 -9.4832860E-02 1,midg,midg; igrid,midg,midg 5.9427854E-02 0.2105755 gauss-seidel spectral radius is 0.9991335 estimated iterations to convergence 268 setup time was (sec) 1.410000 now iterating at: 03:26:31 rms-change max change #iterations 8.690782 258.5745 at 10iterations 4.954865 130.9438 at 20iterations 2.797296 66.18987 at 30iterations 1.575443 37.98302 at 40iterations 0.8763898 21.39236 at 50iterations 0.4880132 11.42629 at 60iterations 0.2698769 5.930747 at 70iterations 0.1496432 3.691112 at 80iterations 8.2492359E-02 1.762817 at 90iterations 4.5455731E-02 1.080925 at 100iterations 2.4985414E-02 0.5922394 at 110iterations 1.3750618E-02 0.2826309 at 120iterations 7.5587202E-03 0.1756363 at 130iterations 4.1561266E-03 8.5212708E-02 at 140iterations 2.2820211E-03 5.0298691E-02 at 150iterations 1.2544169E-03 2.7683258E-02 at 160iterations 6.9012336E-04 1.4806747E-02 at 170iterations 3.8033503E-04 8.5010529E-03 at 180iterations finished qdiffx linear iterations at : 03:26:42 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 3.8033503E-04 8.5010529E-03 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 03:26:42 12.109u 0.276s 0:12.69 97.4% 0+0k 0+0io 0pf+0w