Wed Dec 28 11:01:56 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+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 Wed Dec 28 2011 at 11:01:56 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6546404 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): -4.535000 34.63900 ymin,ymax (A): -3.577000 48.22600 zmin,zma (A): -23.57500 30.80600 x,y,z range (A): 39.17400 51.80300 54.38100 scale (grids/A): 0.6546404 object centre (A): 15.05200 22.32450 3.615500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 90.29772 92.70472 90.00529 assigned negative charge : -284.4403 centred at (gu) : 90.41967 92.85930 89.93063 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5716 nv = 96 ne = 84 npr = 40563 no. pairs analyzed = 40563 no. exposed pairs = 2465 no. arc points = 17125 no. surface atoms = 832 nbur = 1134 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3190 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.2500000 number of dielectric boundary points 2812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1716 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6703 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4166232E-09 1.7279982E-08 midg,1,midg; midg,igrid,midg 1.5429768E-08 -2.1461970E-08 1,midg,midg; igrid,midg,midg 2.1658526E-08 -7.9796107E-09 gauss-seidel spectral radius is 0.9878492 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 11:01:57 rms-change max change #iterations 0.1324529 20.23559 at 10iterations 1.3644192E-02 1.912615 at 20iterations 1.4328089E-03 0.2343969 at 30iterations 1.4563593E-04 2.2365570E-02 at 40iterations 1.5255348E-05 2.3488998E-03 at 50iterations finished qdiffx linear iterations at : 11:02:01 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 1.5255348E-05 2.3488998E-03 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.790000 DelPhi exited at 11:02:03 4.795u 0.517s 0:06.72 78.8% 0+0k 0+0io 6pf+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 11:02:03 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.963921 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): -4.535000 34.63900 ymin,ymax (A): -3.577000 48.22600 zmin,zma (A): -23.57500 30.80600 x,y,z range (A): 39.17400 51.80300 54.38100 scale (grids/A): 1.963921 object centre (A): 15.05200 22.32450 3.615500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 90.89307 98.11438 90.01606 assigned negative charge : -284.4403 centred at (gu) : 91.25941 98.57818 89.79210 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 61628 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17125 grid for indexing accessible points = 1.400000 m= 23067 mr = 42759 m= 3729 mr = 17623 m= 227 mr = 2546 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1756 time to turn everything in is 0.6200000 number of dielectric boundary points 25642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 14475 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) : 0.6546404 object centre at (A) : 15.05200 22.32450 3.615500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0085519E-02 1.5909584E-02 midg,1,midg; midg,igrid,midg 4.8233811E-02 -9.5575294E-03 1,midg,midg; igrid,midg,midg 9.1109248E-03 -6.0231015E-03 gauss-seidel spectral radius is 0.9986346 estimated iterations to convergence 214 setup time was (sec) 1.150000 now iterating at: 11:02:05 rms-change max change #iterations 3.744644 181.3485 at 10iterations 1.759395 68.06105 at 20iterations 0.8263872 29.05817 at 30iterations 0.3845777 12.74817 at 40iterations 0.1811268 6.081708 at 50iterations 8.4138744E-02 3.234299 at 60iterations 3.9476547E-02 1.323795 at 70iterations 1.8530896E-02 0.6152971 at 80iterations 8.6559178E-03 0.2721615 at 90iterations 4.0469957E-03 0.1413574 at 100iterations 1.8974700E-03 6.7491829E-02 at 110iterations 8.8912586E-04 3.4200668E-02 at 120iterations finished qdiffx linear iterations at : 11:02:20 total time elapsed so far: 16.29000 # loops : 120 mean,max change (kT/e) : 8.8912586E-04 3.4200668E-02 energy calculations done at 16.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.46000 DelPhi exited at 11:02:21 16.469u 0.854s 0:17.88 96.8% 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 11:02:21 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.945882 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): -4.535000 34.63900 ymin,ymax (A): -3.577000 48.22600 zmin,zma (A): -23.57500 30.80600 x,y,z range (A): 39.17400 51.80300 54.38100 scale (grids/A): 2.945882 object centre (A): 15.05200 22.32450 3.615500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 91.33963 102.1715 90.02400 assigned negative charge : -284.4403 centred at (gu) : 91.88908 102.8674 89.68822 start vw surface at 0.1100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 142341 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17125 grid for indexing accessible points = 1.400000 m= 73531 mr = 103115 m= 27982 mr = 61362 m= 6936 mr = 23307 m= 1081 mr = 5493 m= 54 mr = 784 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 5911 time to turn everything in is 1.630000 number of dielectric boundary points 57845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.870000 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) : 1.963921 object centre at (A) : 15.05200 22.32450 3.615500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.138894 4.9122360E-02 midg,1,midg; midg,igrid,midg 0.5010798 -0.1621354 1,midg,midg; igrid,midg,midg 5.4942451E-02 -3.1479660E-02 gauss-seidel spectral radius is 0.9992462 estimated iterations to convergence 287 setup time was (sec) 2.220000 now iterating at: 11:02:24 rms-change max change #iterations 8.735793 359.7019 at 10iterations 5.010376 120.4021 at 20iterations 2.858975 60.53049 at 30iterations 1.630852 34.78527 at 40iterations 0.9314518 17.85167 at 50iterations 0.5305406 10.33485 at 60iterations 0.3027118 6.238523 at 70iterations 0.1726670 3.333975 at 80iterations 9.8299466E-02 1.874793 at 90iterations 5.6172680E-02 1.036973 at 100iterations 3.1963971E-02 0.6080933 at 110iterations 1.8210229E-02 0.3958665 at 120iterations 1.0395262E-02 0.2031646 at 130iterations 5.9311953E-03 0.1236267 at 140iterations 3.3800690E-03 6.3657761E-02 at 150iterations 1.9253382E-03 3.7775040E-02 at 160iterations 1.0985931E-03 2.0428181E-02 at 170iterations 6.2802224E-04 1.1848450E-02 at 180iterations finished qdiffx linear iterations at : 11:02:51 total time elapsed so far: 29.42000 # loops : 180 mean,max change (kT/e) : 6.2802224E-04 1.1848450E-02 energy calculations done at 29.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.60000 DelPhi exited at 11:02:52 29.606u 0.965s 0:31.23 97.8% 0+0k 0+0io 0pf+0w