Wed Dec 28 11:04:42 PST 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 Wed Dec 28 2011 at 11:04:42 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6396090 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): -5.443000 34.79500 ymin,ymax (A): -3.745000 48.32500 zmin,zma (A): -24.42500 31.23400 x,y,z range (A): 40.23800 52.07000 55.65900 scale (grids/A): 0.6396090 object centre (A): 14.67600 22.29000 3.404501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.4260 centred at (gu) : 90.72778 92.57001 90.16331 assigned negative charge : -289.4262 centred at (gu) : 90.84618 92.73272 90.09548 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5522 nv = 96 ne = 84 npr = 40372 no. pairs analyzed = 40372 no. exposed pairs = 2483 no. arc points = 17554 no. surface atoms = 836 nbur = 1128 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 3088 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1787 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6518 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3836610E-09 9.4164196E-09 midg,1,midg; midg,igrid,midg 9.8273878E-09 -1.9229063E-08 1,midg,midg; igrid,midg,midg 1.1391736E-08 -8.0985112E-09 gauss-seidel spectral radius is 0.9872804 estimated iterations to convergence 72 setup time was (sec) 0.4600000 now iterating at: 11:04:42 rms-change max change #iterations 0.1260487 22.83987 at 10iterations 1.2556379E-02 1.823814 at 20iterations 1.2359315E-03 0.2320049 at 30iterations 1.2221056E-04 1.9183159E-02 at 40iterations 1.1819526E-05 1.7890930E-03 at 50iterations finished qdiffx linear iterations at : 11:04:45 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 1.1819526E-05 1.7890930E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 11:04:45 3.237u 0.182s 0:03.79 89.9% 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 Wed Dec 28 2011 at 11:04:46 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.918827 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): -5.443000 34.79500 ymin,ymax (A): -3.745000 48.32500 zmin,zma (A): -24.42500 31.23400 x,y,z range (A): 40.23800 52.07000 55.65900 scale (grids/A): 1.918827 object centre (A): 14.67600 22.29000 3.404501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.4260 centred at (gu) : 92.18342 97.71005 90.48987 assigned negative charge : -289.4262 centred at (gu) : 92.53865 98.19823 90.28651 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59151 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17554 grid for indexing accessible points = 1.400000 m= 22490 mr = 40823 m= 3676 mr = 17289 m= 204 mr = 2441 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1308 time to turn everything in is 0.4400000 number of dielectric boundary points 24912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14441 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) : 0.6396090 object centre at (A) : 14.67600 22.29000 3.404501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9661534E-02 1.0242175E-02 midg,1,midg; midg,igrid,midg 3.0875986E-02 -1.8824864E-02 1,midg,midg; igrid,midg,midg 8.2259504E-03 -5.3085373E-03 gauss-seidel spectral radius is 0.9985774 estimated iterations to convergence 210 setup time was (sec) 0.7000000 now iterating at: 11:04:46 rms-change max change #iterations 3.658979 164.2106 at 10iterations 1.685827 56.78448 at 20iterations 0.7789289 26.11196 at 30iterations 0.3602571 12.88691 at 40iterations 0.1652868 6.052801 at 50iterations 7.6175794E-02 2.664799 at 60iterations 3.4981627E-02 1.224081 at 70iterations 1.6141323E-02 0.5223331 at 80iterations 7.4541960E-03 0.2625542 at 90iterations 3.4241111E-03 0.1242654 at 100iterations 1.5775567E-03 6.0413361E-02 at 110iterations 7.2974747E-04 2.4719238E-02 at 120iterations finished qdiffx linear iterations at : 11:04:52 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 7.2974747E-04 2.4719238E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.800000 DelPhi exited at 11:04:53 6.800u 0.187s 0:07.56 92.3% 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 Wed Dec 28 2011 at 11:04:53 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.878241 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): -5.443000 34.79500 ymin,ymax (A): -3.745000 48.32500 zmin,zma (A): -24.42500 31.23400 x,y,z range (A): 40.23800 52.07000 55.65900 scale (grids/A): 2.878241 object centre (A): 14.67600 22.29000 3.404501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.4260 centred at (gu) : 93.27512 101.5650 90.73486 assigned negative charge : -289.4262 centred at (gu) : 93.80800 102.2975 90.42988 start vw surface at 0.1200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 136432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17554 grid for indexing accessible points = 1.400000 m= 71114 mr = 98330 m= 27452 mr = 59413 m= 6767 mr = 22874 m= 879 mr = 5294 m= 47 mr = 608 m= 0 mr = 10 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 4607 time to turn everything in is 1.210000 number of dielectric boundary points 56162 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 14656 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) : 1.918827 object centre at (A) : 14.67600 22.29000 3.404501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9786820 -1.2363800E-02 midg,1,midg; midg,igrid,midg 0.3400785 -0.2047425 1,midg,midg; igrid,midg,midg 4.6691880E-02 -3.5578612E-02 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.530000 now iterating at: 11:04:55 rms-change max change #iterations 8.616778 488.5248 at 10iterations 4.942879 122.8578 at 20iterations 2.807109 61.49105 at 30iterations 1.594066 33.17412 at 40iterations 0.9045407 18.68839 at 50iterations 0.5145245 10.20992 at 60iterations 0.2910258 5.797731 at 70iterations 0.1652397 3.222454 at 80iterations 9.3815863E-02 1.935386 at 90iterations 5.3161960E-02 1.005838 at 100iterations 3.0201618E-02 0.6014776 at 110iterations 1.7087091E-02 0.3495603 at 120iterations 9.7144237E-03 0.2023468 at 130iterations 5.4991171E-03 0.1128693 at 140iterations 3.1169513E-03 6.1197281E-02 at 150iterations 1.7677357E-03 3.4660339E-02 at 160iterations 1.0021230E-03 1.9561768E-02 at 170iterations 5.6844403E-04 1.1152267E-02 at 180iterations finished qdiffx linear iterations at : 11:05:05 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 5.6844403E-04 1.1152267E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.78000 DelPhi exited at 11:05:06 11.784u 0.299s 0:12.47 96.7% 0+0k 0+0io 0pf+0w