Tue Nov 22 14:12:28 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 Tue Nov 22 2011 at 14:12:32 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5500958 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): -34.93400 11.93900 ymin,ymax (A): 0.1070000 42.50200 zmin,zma (A): -4.329000 60.38700 x,y,z range (A): 46.87300 42.39500 64.71600 scale (grids/A): 0.5500958 object centre (A): -11.49750 21.30450 28.02900 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 293.7999 centred at (gu) : 89.86899 89.46388 89.91740 assigned negative charge : -290.8002 centred at (gu) : 89.80340 89.57309 89.91019 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 3925 nv = 96 ne = 84 npr = 39720 no. pairs analyzed = 39720 no. exposed pairs = 2525 no. arc points = 18025 no. surface atoms = 850 nbur = 1120 mkacc time = 9.0000004E-02 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= 138 mr = 2027 m= 0 mr = 7 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2200000 number of dielectric boundary points 2029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1806 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5025 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8388500E-10 2.4845265E-10 midg,1,midg; midg,igrid,midg 8.7117930E-10 -2.9988886E-10 1,midg,midg; igrid,midg,midg -1.2256564E-10 5.2935006E-10 gauss-seidel spectral radius is 0.9828811 estimated iterations to convergence 63 setup time was (sec) 0.4500000 now iterating at: 14:12:35 rms-change max change #iterations 6.2634453E-02 13.43470 at 10iterations 4.1638329E-03 0.8503420 at 20iterations 2.9005067E-04 6.2557220E-02 at 30iterations 1.9263345E-05 4.2788982E-03 at 40iterations 1.3252182E-06 2.7084351E-04 at 50iterations finished qdiffx linear iterations at : 14:12:43 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.3252182E-06 2.7084351E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 14:12:45 3.163u 0.145s 0:13.80 23.9% 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 Nov 22 2011 at 14:12:47 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.650287 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): -34.93400 11.93900 ymin,ymax (A): 0.1070000 42.50200 zmin,zma (A): -4.329000 60.38700 x,y,z range (A): 46.87300 42.39500 64.71600 scale (grids/A): 1.650287 object centre (A): -11.49750 21.30450 28.02900 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 293.7999 centred at (gu) : 89.60719 88.39194 89.75230 assigned negative charge : -290.8002 centred at (gu) : 89.41053 88.71951 89.73062 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 42910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18025 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 13488 mr = 28432 m= 1405 mr = 9676 m= 44 mr = 741 m= 0 mr = 13 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 980 time to turn everything in is 0.3100000 number of dielectric boundary points 18985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14109 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) : 0.5500958 object centre at (A) : -11.49750 21.30450 28.02900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6690455E-02 1.4964295E-02 midg,1,midg; midg,igrid,midg 2.0100218E-03 -3.4246841E-03 1,midg,midg; igrid,midg,midg -5.7576504E-04 -3.9732366E-04 gauss-seidel spectral radius is 0.9981031 estimated iterations to convergence 182 setup time was (sec) 0.5800000 now iterating at: 14:12:52 rms-change max change #iterations 2.710804 155.2795 at 10iterations 1.106368 50.17617 at 20iterations 0.4540483 20.92447 at 30iterations 0.1847737 8.337914 at 40iterations 7.5587980E-02 3.085211 at 50iterations 3.0788848E-02 1.277192 at 60iterations 1.2571732E-02 0.5611496 at 70iterations 5.1261052E-03 0.2236875 at 80iterations 2.1054482E-03 9.1459274E-02 at 90iterations 8.6238910E-04 3.5413265E-02 at 100iterations 3.5139068E-04 1.5922546E-02 at 110iterations 1.4403700E-04 6.4086914E-03 at 120iterations finished qdiffx linear iterations at : 14:13:10 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 1.4403700E-04 6.4086914E-03 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 14:13:11 6.810u 0.210s 0:23.17 30.2% 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 Tue Nov 22 2011 at 14:13:11 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.475431 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): -34.93400 11.93900 ymin,ymax (A): 0.1070000 42.50200 zmin,zma (A): -4.329000 60.38700 x,y,z range (A): 46.87300 42.39500 64.71600 scale (grids/A): 2.475431 object centre (A): -11.49750 21.30450 28.02900 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 293.7999 centred at (gu) : 89.41069 87.58778 89.62836 assigned negative charge : -290.8002 centred at (gu) : 89.11583 88.07935 89.59602 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 99262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18025 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 46269 mr = 69185 m= 13954 mr = 37192 m= 2342 mr = 11055 m= 191 mr = 1592 m= 4 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 3446 time to turn everything in is 0.7500000 number of dielectric boundary points 42903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14690 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) : 1.650287 object centre at (A) : -11.49750 21.30450 28.02900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1945838 0.1513959 midg,1,midg; midg,igrid,midg 5.0326891E-04 -6.1090503E-02 1,midg,midg; igrid,midg,midg -2.6426446E-02 -1.8566333E-02 gauss-seidel spectral radius is 0.9990765 estimated iterations to convergence 260 setup time was (sec) 1.030000 now iterating at: 14:13:12 rms-change max change #iterations 6.878924 308.3000 at 10iterations 3.738377 100.9698 at 20iterations 2.019948 62.19908 at 30iterations 1.086668 27.05564 at 40iterations 0.5845397 14.77207 at 50iterations 0.3140028 8.565407 at 60iterations 0.1690734 4.021893 at 70iterations 9.0758614E-02 2.225037 at 80iterations 4.8619445E-02 1.132343 at 90iterations 2.6089404E-02 0.6441007 at 100iterations 1.4003214E-02 0.3606262 at 110iterations 7.5093280E-03 0.1763754 at 120iterations 4.0310025E-03 0.1023855 at 130iterations 2.1584963E-03 5.0376892E-02 at 140iterations 1.1605240E-03 3.0280113E-02 at 150iterations 6.2212488E-04 1.4802456E-02 at 160iterations 3.3417196E-04 7.6646805E-03 at 170iterations 1.7864347E-04 4.2495728E-03 at 180iterations finished qdiffx linear iterations at : 14:13:30 total time elapsed so far: 10.29000 # loops : 180 mean,max change (kT/e) : 1.7864347E-04 4.2495728E-03 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.46000 DelPhi exited at 14:13:32 10.458u 0.205s 0:21.76 48.9% 0+0k 0+0io 0pf+0w