Sat Oct 15 12:22:10 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 Sat Oct 15 2011 at 12:22:10 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5210469 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): 220.0680 276.2330 ymin,ymax (A): 71.91800 140.2420 zmin,zma (A): -70.25900 -6.132000 x,y,z range (A): 56.16499 68.32399 64.12700 scale (grids/A): 0.5210469 object centre (A): 248.1505 106.0800 -38.19550 number of atom coordinates read : 4556 total number of charged atoms : 4398 net assigned charge : 17.49998 assigned positive charge : 676.7885 centred at (gu) : 90.08562 87.40529 90.94734 assigned negative charge : -659.2939 centred at (gu) : 90.14544 87.40919 91.02652 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7697 nv = 96 ne = 84 npr = 92015 no. pairs analyzed = 92015 no. exposed pairs = 5962 no. arc points = 39973 no. surface atoms = 2036 nbur = 2520 mkacc time = 0.2400000 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 = 1.624000 m= 319 mr = 3864 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3979 ## 548 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 10412 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3363519E-10 1.1979956E-10 midg,1,midg; midg,igrid,midg 7.8712226E-10 1.9870178E-10 1,midg,midg; igrid,midg,midg 5.9616884E-10 1.7349193E-10 gauss-seidel spectral radius is 0.9811451 estimated iterations to convergence 60 setup time was (sec) 0.8600000 now iterating at: 12:22:12 rms-change max change #iterations 7.4231602E-02 11.60439 at 10iterations 5.9594954E-03 0.8589840 at 20iterations 1.4418134E-03 0.1913033 at 30iterations 4.9554073E-04 6.2686920E-02 at 40iterations 1.7453407E-04 2.3344994E-02 at 50iterations finished qdiffx linear iterations at : 12:22:16 total time elapsed so far: 5.330000 # loops : 50 mean,max change (kT/e) : 1.7453407E-04 2.3344994E-02 energy calculations done at 5.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.510000 DelPhi exited at 12:22:17 5.511u 0.457s 0:06.26 95.2% 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 12:22:17 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.563141 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): 220.0680 276.2330 ymin,ymax (A): 71.91800 140.2420 zmin,zma (A): -70.25900 -6.132000 x,y,z range (A): 56.16499 68.32399 64.12700 scale (grids/A): 1.563141 object centre (A): 248.1505 106.0800 -38.19550 number of atom coordinates read : 4556 total number of charged atoms : 4398 net assigned charge : 17.49998 assigned positive charge : 676.7885 centred at (gu) : 90.25498 82.21436 92.84026 assigned negative charge : -659.2939 centred at (gu) : 90.43617 82.22726 93.07968 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 86051 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39973 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 25966 mr = 57552 m= 2347 mr = 17173 m= 45 mr = 1004 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 620 time to turn everything in is 0.7700000 number of dielectric boundary points 38680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 497 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 33318 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) : 0.5210469 object centre at (A) : 248.1505 106.0800 -38.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1759482E-02 6.7574671E-03 midg,1,midg; midg,igrid,midg 3.2389142E-02 1.1351113E-02 1,midg,midg; igrid,midg,midg 3.9326758E-03 4.3991110E-03 gauss-seidel spectral radius is 0.9981732 estimated iterations to convergence 186 setup time was (sec) 1.170000 now iterating at: 12:22:18 rms-change max change #iterations 3.787285 158.6961 at 10iterations 1.569635 54.55125 at 20iterations 0.6495348 20.67382 at 30iterations 0.2705633 8.737727 at 40iterations 0.1127093 3.541955 at 50iterations 4.7355015E-02 1.663555 at 60iterations 1.9962529E-02 0.6283643 at 70iterations 8.7485537E-03 0.2955239 at 80iterations 4.0765097E-03 0.1232727 at 90iterations 2.1048845E-03 6.6656351E-02 at 100iterations 1.2266409E-03 3.4065247E-02 at 110iterations 7.8504940E-04 2.1541595E-02 at 120iterations finished qdiffx linear iterations at : 12:22:30 total time elapsed so far: 12.95000 # loops : 120 mean,max change (kT/e) : 7.8504940E-04 2.1541595E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 12:22:31 13.135u 0.545s 0:13.95 97.9% 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 Sat Oct 15 2011 at 12:22:31 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.344711 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): 220.0680 276.2330 ymin,ymax (A): 71.91800 140.2420 zmin,zma (A): -70.25900 -6.132000 x,y,z range (A): 56.16499 68.32399 64.12700 scale (grids/A): 2.344711 object centre (A): 248.1505 106.0800 -38.19550 number of atom coordinates read : 4556 total number of charged atoms : 4398 net assigned charge : 17.49998 assigned positive charge : 676.7885 centred at (gu) : 90.38203 78.32102 94.26001 assigned negative charge : -659.2939 centred at (gu) : 90.65417 78.34074 94.61938 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 199907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39973 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 89842 mr = 141442 m= 24852 mr = 69465 m= 3491 mr = 18237 m= 171 mr = 2039 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 2227 time to turn everything in is 1.860000 number of dielectric boundary points 87028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 35099 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) : 1.563141 object centre at (A) : 248.1505 106.0800 -38.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4927375 4.3532498E-02 midg,1,midg; midg,igrid,midg 0.4708156 0.1610227 1,midg,midg; igrid,midg,midg 6.1550502E-02 3.8946629E-02 gauss-seidel spectral radius is 0.9991742 estimated iterations to convergence 275 setup time was (sec) 2.280000 now iterating at: 12:22:33 rms-change max change #iterations 10.23262 335.1914 at 10iterations 5.904021 162.8566 at 20iterations 3.375480 75.55191 at 30iterations 1.920881 37.58611 at 40iterations 1.085095 23.49869 at 50iterations 0.6113754 13.35588 at 60iterations 0.3434223 6.735087 at 70iterations 0.1931570 3.933202 at 80iterations 0.1082932 2.112511 at 90iterations 6.0565654E-02 1.264072 at 100iterations 3.3881489E-02 0.6577196 at 110iterations 1.9027660E-02 0.3613467 at 120iterations 1.0674017E-02 0.1920300 at 130iterations 6.0459832E-03 0.1098303 at 140iterations 3.4538982E-03 6.3268661E-02 at 150iterations 2.0150959E-03 3.7826538E-02 at 160iterations 1.2166122E-03 2.1292686E-02 at 170iterations 7.6913275E-04 1.4442444E-02 at 180iterations finished qdiffx linear iterations at : 12:22:54 total time elapsed so far: 22.66000 # loops : 180 mean,max change (kT/e) : 7.6913275E-04 1.4442444E-02 energy calculations done at 22.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.84000 DelPhi exited at 12:22:54 22.846u 0.565s 0:23.66 98.9% 0+0k 0+0io 0pf+0w