Sat Oct 8 17:04:16 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 8 2011 at 17:04:16 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3524 !!! WARNING: ASL 226 has a net charge of -0.1000 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: 0.5357815 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): -2.226000 64.21900 ymin,ymax (A): 14.60600 76.28600 zmin,zma (A): -13.57500 34.87400 x,y,z range (A): 66.44500 61.68000 48.44900 scale (grids/A): 0.5357815 object centre (A): 30.99650 45.44600 10.64950 number of atom coordinates read : 3524 total number of charged atoms : 3378 net assigned charge : -6.099988 assigned positive charge : 538.7492 centred at (gu) : 89.27919 87.13526 89.51305 assigned negative charge : -544.8509 centred at (gu) : 89.26292 87.13383 89.52773 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6408 nv = 96 ne = 84 npr = 72076 no. pairs analyzed = 72076 no. exposed pairs = 4299 no. arc points = 29491 no. surface atoms = 1451 nbur = 2073 mkacc time = 0.1900000 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= 280 mr = 3455 m= 0 mr = 9 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2991 ## 405 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8563 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9056920E-10 -2.9250949E-10 midg,1,midg; midg,igrid,midg -5.2517352E-10 -1.2155182E-10 1,midg,midg; igrid,midg,midg -4.0490183E-10 -1.3570954E-10 gauss-seidel spectral radius is 0.9820814 estimated iterations to convergence 62 setup time was (sec) 0.6800000 now iterating at: 17:04:17 rms-change max change #iterations 7.6377757E-02 13.15633 at 10iterations 4.8962431E-03 0.7222307 at 20iterations 3.4199518E-04 6.0115814E-02 at 30iterations 4.4306205E-05 9.3045235E-03 at 40iterations 9.9165827E-06 2.2692680E-03 at 50iterations finished qdiffx linear iterations at : 17:04:21 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 9.9165827E-06 2.2692680E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 17:04:21 4.622u 0.403s 0:05.28 95.0% 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 Sat Oct 8 2011 at 17:04:21 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3524 !!! WARNING: ASL 226 has a net charge of -0.1000 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: 1.607344 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): -2.226000 64.21900 ymin,ymax (A): 14.60600 76.28600 zmin,zma (A): -13.57500 34.87400 x,y,z range (A): 66.44500 61.68000 48.44900 scale (grids/A): 1.607344 object centre (A): 30.99650 45.44600 10.64950 number of atom coordinates read : 3524 total number of charged atoms : 3378 net assigned charge : -6.099988 assigned positive charge : 538.7492 centred at (gu) : 87.83655 81.40533 88.53809 assigned negative charge : -544.8509 centred at (gu) : 87.78841 81.40101 88.58268 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22224 mr = 50111 m= 2161 mr = 15314 m= 52 mr = 960 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 0.5800000 number of dielectric boundary points 30010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 378 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25759 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) : 0.5357815 object centre at (A) : 30.99650 45.44600 10.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3014584E-04 -8.5790205E-04 midg,1,midg; midg,igrid,midg -2.1198383E-02 -1.4345644E-02 1,midg,midg; igrid,midg,midg 5.2850419E-03 -3.9496631E-03 gauss-seidel spectral radius is 0.9981613 estimated iterations to convergence 185 setup time was (sec) 0.8700000 now iterating at: 17:04:23 rms-change max change #iterations 3.587634 159.3635 at 10iterations 1.486853 51.90770 at 20iterations 0.6164420 21.35780 at 30iterations 0.2563976 10.70928 at 40iterations 0.1067570 3.669731 at 50iterations 4.4372953E-02 1.448082 at 60iterations 1.8420400E-02 0.6547278 at 70iterations 7.6420712E-03 0.2765670 at 80iterations 3.1875980E-03 0.1120777 at 90iterations 1.3271836E-03 5.0132632E-02 at 100iterations 5.6076626E-04 2.1255493E-02 at 110iterations 2.3953344E-04 8.8820159E-03 at 120iterations finished qdiffx linear iterations at : 17:04:32 total time elapsed so far: 10.20000 # loops : 120 mean,max change (kT/e) : 2.3953344E-04 8.8820159E-03 energy calculations done at 10.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.35000 DelPhi exited at 17:04:33 10.355u 0.480s 0:11.08 97.7% 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 Sat Oct 8 2011 at 17:04:33 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3524 !!! WARNING: ASL 226 has a net charge of -0.1000 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: 2.411017 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): -2.226000 64.21900 ymin,ymax (A): 14.60600 76.28600 zmin,zma (A): -13.57500 34.87400 x,y,z range (A): 66.44500 61.68000 48.44900 scale (grids/A): 2.411017 object centre (A): 30.99650 45.44600 10.64950 number of atom coordinates read : 3524 total number of charged atoms : 3378 net assigned charge : -6.099988 assigned positive charge : 538.7492 centred at (gu) : 86.75484 77.10754 87.80708 assigned negative charge : -544.8509 centred at (gu) : 86.68251 77.10151 87.87392 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 77684 mr = 122136 m= 21398 mr = 61868 m= 3400 mr = 15923 m= 177 mr = 2182 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 67650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 26985 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) : 1.607344 object centre at (A) : 30.99650 45.44600 10.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5748180E-02 -1.2123062E-02 midg,1,midg; midg,igrid,midg -0.4110948 -0.2740571 1,midg,midg; igrid,midg,midg 0.3688317 -5.9283461E-02 gauss-seidel spectral radius is 0.9991344 estimated iterations to convergence 269 setup time was (sec) 1.830000 now iterating at: 17:04:35 rms-change max change #iterations 9.353270 293.6651 at 10iterations 5.249107 141.1315 at 20iterations 2.930433 67.50372 at 30iterations 1.630315 35.13929 at 40iterations 0.9021106 18.57467 at 50iterations 0.4983486 10.92441 at 60iterations 0.2750934 5.455381 at 70iterations 0.1516439 3.059717 at 80iterations 8.3468892E-02 1.627331 at 90iterations 4.5918930E-02 0.9281006 at 100iterations 2.5213260E-02 0.5085354 at 110iterations 1.3884485E-02 0.2781839 at 120iterations 7.6256534E-03 0.1702738 at 130iterations 4.1997158E-03 8.5912704E-02 at 140iterations 2.3127107E-03 4.5581818E-02 at 150iterations 1.2778698E-03 2.4619684E-02 at 160iterations 7.1076269E-04 1.4718831E-02 at 170iterations 3.9966026E-04 7.9860687E-03 at 180iterations finished qdiffx linear iterations at : 17:04:51 total time elapsed so far: 17.67000 # loops : 180 mean,max change (kT/e) : 3.9966026E-04 7.9860687E-03 energy calculations done at 17.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.85000 DelPhi exited at 17:04:51 17.850u 0.461s 0:18.56 98.6% 0+0k 0+0io 0pf+0w