Mon Oct 10 19:20:18 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+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 Mon Oct 10 2011 at 19:20:18 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2349 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: 0.6087551 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): -18.37000 33.37100 ymin,ymax (A): -21.07800 23.85900 zmin,zma (A): -30.25000 28.23000 x,y,z range (A): 51.74100 44.93700 58.48000 scale (grids/A): 0.6087551 object centre (A): 7.500502 1.390500 -1.010000 number of atom coordinates read : 2349 total number of charged atoms : 2214 net assigned charge : -1.999995 assigned positive charge : 341.2064 centred at (gu) : 90.03793 90.26861 90.19005 assigned negative charge : -343.2070 centred at (gu) : 90.02100 90.23982 90.21740 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5730 nv = 96 ne = 84 npr = 47987 no. pairs analyzed = 47987 no. exposed pairs = 3069 no. arc points = 21112 no. surface atoms = 1055 nbur = 1294 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 3000 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2087 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0508348E-11 -2.3937565E-09 midg,1,midg; midg,igrid,midg -2.2188285E-09 8.2126306E-11 1,midg,midg; igrid,midg,midg -1.8373888E-09 -4.2687354E-10 gauss-seidel spectral radius is 0.9860116 estimated iterations to convergence 69 setup time was (sec) 0.5400000 now iterating at: 19:20:19 rms-change max change #iterations 0.1075710 16.05471 at 10iterations 9.1336509E-03 1.367284 at 20iterations 8.3514414E-04 0.1162033 at 30iterations 7.9801124E-05 1.2225509E-02 at 40iterations 1.3633493E-05 3.0479431E-03 at 50iterations finished qdiffx linear iterations at : 19:20:22 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.3633493E-05 3.0479431E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 19:20:23 3.523u 0.188s 0:04.26 86.8% 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 Mon Oct 10 2011 at 19:20:23 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2349 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: 1.826265 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): -18.37000 33.37100 ymin,ymax (A): -21.07800 23.85900 zmin,zma (A): -30.25000 28.23000 x,y,z range (A): 51.74100 44.93700 58.48000 scale (grids/A): 1.826265 object centre (A): 7.500502 1.390500 -1.010000 number of atom coordinates read : 2349 total number of charged atoms : 2214 net assigned charge : -1.999995 assigned positive charge : 341.2064 centred at (gu) : 90.11349 90.80540 90.56948 assigned negative charge : -343.2070 centred at (gu) : 90.06279 90.71933 90.65229 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21112 grid for indexing accessible points = 1.400000 m= 21171 mr = 42142 m= 3293 mr = 14952 m= 166 mr = 1916 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 27903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17343 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) : 0.6087551 object centre at (A) : 7.500502 1.390500 -1.010000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3928573E-02 -4.0331557E-02 midg,1,midg; midg,igrid,midg 3.1510074E-04 2.6904893E-04 1,midg,midg; igrid,midg,midg -1.5094579E-02 1.5441182E-02 gauss-seidel spectral radius is 0.9984952 estimated iterations to convergence 204 setup time was (sec) 0.8000000 now iterating at: 19:20:24 rms-change max change #iterations 3.618464 197.8192 at 10iterations 1.622263 70.20560 at 20iterations 0.7287561 24.79121 at 30iterations 0.3294179 12.24581 at 40iterations 0.1482844 5.406409 at 50iterations 6.6849880E-02 2.179499 at 60iterations 3.0009739E-02 0.9866543 at 70iterations 1.3544212E-02 0.4805813 at 80iterations 6.1054495E-03 0.2209930 at 90iterations 2.7533129E-03 9.7988129E-02 at 100iterations 1.2432560E-03 4.6976089E-02 at 110iterations 5.6359428E-04 2.1344185E-02 at 120iterations finished qdiffx linear iterations at : 19:20:31 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 5.6359428E-04 2.1344185E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 19:20:31 7.946u 0.248s 0:08.73 93.6% 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 19:20:31 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2349 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: 2.739398 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): -18.37000 33.37100 ymin,ymax (A): -21.07800 23.85900 zmin,zma (A): -30.25000 28.23000 x,y,z range (A): 51.74100 44.93700 58.48000 scale (grids/A): 2.739398 object centre (A): 7.500502 1.390500 -1.010000 number of atom coordinates read : 2349 total number of charged atoms : 2214 net assigned charge : -1.999995 assigned positive charge : 341.2064 centred at (gu) : 90.17003 91.20809 90.85420 assigned negative charge : -343.2070 centred at (gu) : 90.09429 91.07890 90.97848 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 144747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21112 grid for indexing accessible points = 1.400000 m= 68597 mr = 103171 m= 24295 mr = 54630 m= 5871 mr = 18922 m= 802 mr = 4257 m= 28 mr = 486 m= 0 mr = 8 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 62866 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 17711 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) : 1.826265 object centre at (A) : 7.500502 1.390500 -1.010000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4953108 -0.6688931 midg,1,midg; midg,igrid,midg -1.2561982E-02 -3.6061678E-02 1,midg,midg; igrid,midg,midg -0.2610207 0.2389073 gauss-seidel spectral radius is 0.9992170 estimated iterations to convergence 282 setup time was (sec) 1.550000 now iterating at: 19:20:33 rms-change max change #iterations 8.794314 416.0947 at 10iterations 5.082623 121.8335 at 20iterations 2.914746 64.69437 at 30iterations 1.671808 37.98501 at 40iterations 0.9561337 23.90042 at 50iterations 0.5434462 11.30391 at 60iterations 0.3094578 6.962765 at 70iterations 0.1759675 3.842126 at 80iterations 9.9832073E-02 2.090448 at 90iterations 5.6596842E-02 1.137076 at 100iterations 3.2130837E-02 0.6307753 at 110iterations 1.8202344E-02 0.3570037 at 120iterations 1.0305614E-02 0.2023792 at 130iterations 5.8420072E-03 0.1291313 at 140iterations 3.3089030E-03 7.0163488E-02 at 150iterations 1.8759458E-03 3.7036896E-02 at 160iterations 1.0660228E-03 2.3486972E-02 at 170iterations 6.0680107E-04 1.1639595E-02 at 180iterations finished qdiffx linear iterations at : 19:20:44 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 6.0680107E-04 1.1639595E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 19:20:45 12.872u 0.250s 0:13.41 97.8% 0+0k 0+0io 0pf+0w