Mon Oct 10 17:13:00 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 Mon Oct 10 2011 at 17:13:01 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6062670 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): 13.85300 70.72500 ymin,ymax (A): 3.829000 50.92400 zmin,zma (A): 6.930000 65.65000 x,y,z range (A): 56.87200 47.09500 58.72000 scale (grids/A): 0.6062670 object centre (A): 42.28900 27.37650 36.29000 number of atom coordinates read : 2986 total number of charged atoms : 2841 net assigned charge : -5.485974 assigned positive charge : 453.1829 centred at (gu) : 89.19612 90.43582 90.37965 assigned negative charge : -458.6701 centred at (gu) : 89.11520 90.52913 90.49246 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7298 nv = 96 ne = 84 npr = 59614 no. pairs analyzed = 59614 no. exposed pairs = 3906 no. arc points = 27785 no. surface atoms = 1328 nbur = 1658 mkacc time = 0.1500000 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 = 1.456000 m= 319 mr = 3774 m= 0 mr = 12 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3400000 number of dielectric boundary points 3831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9132 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7715392E-09 -9.5311501E-09 midg,1,midg; midg,igrid,midg 1.8341942E-09 -8.5005061E-09 1,midg,midg; igrid,midg,midg -8.4453600E-09 1.1486707E-09 gauss-seidel spectral radius is 0.9859564 estimated iterations to convergence 69 setup time was (sec) 0.6400000 now iterating at: 17:13:02 rms-change max change #iterations 0.1225893 18.43650 at 10iterations 1.0785963E-02 1.493809 at 20iterations 9.2467578E-04 0.1246223 at 30iterations 8.1803802E-05 1.1192322E-02 at 40iterations 7.3794813E-06 1.1253357E-03 at 50iterations finished qdiffx linear iterations at : 17:13:08 total time elapsed so far: 6.930000 # loops : 50 mean,max change (kT/e) : 7.3794813E-06 1.1253357E-03 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 17:13:09 7.099u 0.549s 0:08.19 93.1% 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 Mon Oct 10 2011 at 17:13:09 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.818801 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): 13.85300 70.72500 ymin,ymax (A): 3.829000 50.92400 zmin,zma (A): 6.930000 65.65000 x,y,z range (A): 56.87200 47.09500 58.72000 scale (grids/A): 1.818801 object centre (A): 42.28900 27.37650 36.29000 number of atom coordinates read : 2986 total number of charged atoms : 2841 net assigned charge : -5.485974 assigned positive charge : 453.1829 centred at (gu) : 87.58775 91.30666 91.13803 assigned negative charge : -458.6701 centred at (gu) : 87.34518 91.58695 91.47700 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 79613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27785 grid for indexing accessible points = 1.400000 m= 25632 mr = 53405 m= 3244 mr = 17814 m= 139 mr = 1804 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 984 time to turn everything in is 0.7600000 number of dielectric boundary points 35578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 22238 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) : 0.6062670 object centre at (A) : 42.28900 27.37650 36.29000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9808693E-02 -2.4946500E-04 midg,1,midg; midg,igrid,midg -2.8030206E-03 -2.5306188E-02 1,midg,midg; igrid,midg,midg -4.1166198E-02 1.3525241E-02 gauss-seidel spectral radius is 0.9985538 estimated iterations to convergence 208 setup time was (sec) 1.300000 now iterating at: 17:13:11 rms-change max change #iterations 4.263742 187.2735 at 10iterations 1.943588 67.08218 at 20iterations 0.8866123 32.14294 at 30iterations 0.4046783 13.75889 at 40iterations 0.1853456 5.868279 at 50iterations 8.4881015E-02 2.788986 at 60iterations 3.8718540E-02 1.241601 at 70iterations 1.7740976E-02 0.5732058 at 80iterations 8.1083393E-03 0.2586784 at 90iterations 3.7227576E-03 0.1189575 at 100iterations 1.6986537E-03 5.5816650E-02 at 110iterations 7.7615160E-04 2.3057938E-02 at 120iterations finished qdiffx linear iterations at : 17:13:28 total time elapsed so far: 18.17000 # loops : 120 mean,max change (kT/e) : 7.7615160E-04 2.3057938E-02 energy calculations done at 18.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.34000 DelPhi exited at 17:13:28 18.344u 0.934s 0:19.65 98.0% 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 Mon Oct 10 2011 at 17:13:28 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.728202 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): 13.85300 70.72500 ymin,ymax (A): 3.829000 50.92400 zmin,zma (A): 6.930000 65.65000 x,y,z range (A): 56.87200 47.09500 58.72000 scale (grids/A): 2.728202 object centre (A): 42.28900 27.37650 36.29000 number of atom coordinates read : 2986 total number of charged atoms : 2841 net assigned charge : -5.485974 assigned positive charge : 453.1829 centred at (gu) : 86.38131 91.95998 91.70691 assigned negative charge : -458.6701 centred at (gu) : 86.01780 92.38030 92.21524 start vw surface at 0.1400000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 184530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27785 grid for indexing accessible points = 1.400000 m= 86427 mr = 130568 m= 27512 mr = 68514 m= 5418 mr = 21003 m= 530 mr = 3764 m= 22 mr = 299 m= 0 mr = 4 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 3227 time to turn everything in is 1.960000 number of dielectric boundary points 80287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 22722 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) : 1.818801 object centre at (A) : 42.28900 27.37650 36.29000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3187082 0.1912965 midg,1,midg; midg,igrid,midg -4.4888180E-02 -0.2491225 1,midg,midg; igrid,midg,midg -0.4628343 0.2720621 gauss-seidel spectral radius is 0.9992563 estimated iterations to convergence 289 setup time was (sec) 2.610000 now iterating at: 17:13:32 rms-change max change #iterations 10.43050 325.7177 at 10iterations 6.155849 142.3417 at 20iterations 3.588107 84.11353 at 30iterations 2.080229 42.53165 at 40iterations 1.206360 23.38679 at 50iterations 0.6961055 14.40483 at 60iterations 0.4018629 8.528449 at 70iterations 0.2308849 4.349043 at 80iterations 0.1327719 2.445243 at 90iterations 7.6360866E-02 1.758633 at 100iterations 4.3850634E-02 0.8487716 at 110iterations 2.5216790E-02 0.4728909 at 120iterations 1.4469496E-02 0.2934408 at 130iterations 8.2982359E-03 0.1551785 at 140iterations 4.7656456E-03 8.4936142E-02 at 150iterations 2.7307656E-03 5.2423477E-02 at 160iterations 1.5711028E-03 3.1049013E-02 at 170iterations 9.0360554E-04 1.9497871E-02 at 180iterations finished qdiffx linear iterations at : 17:14:02 total time elapsed so far: 32.19000 # loops : 180 mean,max change (kT/e) : 9.0360554E-04 1.9497871E-02 energy calculations done at 32.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 32.37000 DelPhi exited at 17:14:02 32.378u 0.889s 0:33.71 98.6% 0+0k 0+0io 0pf+0w