Mon Oct 10 19:40:16 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 19:40:16 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 = 2306 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: 0.6292644 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): 18.91600 65.78700 ymin,ymax (A): 11.18300 55.33500 zmin,zma (A): -0.2020000 56.37200 x,y,z range (A): 46.87100 44.15200 56.57400 scale (grids/A): 0.6292644 object centre (A): 42.35150 33.25900 28.08500 number of atom coordinates read : 2306 total number of charged atoms : 2171 net assigned charge : -1.999993 assigned positive charge : 333.1694 centred at (gu) : 90.81406 90.04235 88.87449 assigned negative charge : -335.1703 centred at (gu) : 90.81841 90.01894 88.92847 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6231 nv = 96 ne = 84 npr = 47057 no. pairs analyzed = 47057 no. exposed pairs = 2943 no. arc points = 20646 no. surface atoms = 1001 nbur = 1305 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 343 mr = 3393 m= 5 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2700000 number of dielectric boundary points 3142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1949 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7388 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3970848E-09 -4.8848894E-09 midg,1,midg; midg,igrid,midg -3.8909644E-09 -4.3095036E-10 1,midg,midg; igrid,midg,midg -1.5610606E-09 -2.9705929E-09 gauss-seidel spectral radius is 0.9868957 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 19:40:16 rms-change max change #iterations 0.1240149 19.20651 at 10iterations 1.1836550E-02 2.113805 at 20iterations 1.1377446E-03 0.1554794 at 30iterations 1.1863557E-04 1.5975952E-02 at 40iterations 1.7211838E-05 2.5930405E-03 at 50iterations finished qdiffx linear iterations at : 19:40:19 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.7211838E-05 2.5930405E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 19:40:19 3.258u 0.180s 0:03.72 92.2% 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 Mon Oct 10 2011 at 19:40:19 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 = 2306 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: 1.887793 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): 18.91600 65.78700 ymin,ymax (A): 11.18300 55.33500 zmin,zma (A): -0.2020000 56.37200 x,y,z range (A): 46.87100 44.15200 56.57400 scale (grids/A): 1.887793 object centre (A): 42.35150 33.25900 28.08500 number of atom coordinates read : 2306 total number of charged atoms : 2171 net assigned charge : -1.999993 assigned positive charge : 333.1694 centred at (gu) : 92.44194 90.12672 86.62312 assigned negative charge : -335.1703 centred at (gu) : 92.45572 90.05706 86.78555 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20646 grid for indexing accessible points = 1.400000 m= 23913 mr = 46777 m= 3923 mr = 17448 m= 224 mr = 2336 m= 3 mr = 75 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 0.5000000 number of dielectric boundary points 28790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 17075 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) : 0.6292644 object centre at (A) : 42.35150 33.25900 28.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4017619E-02 -3.8223650E-02 midg,1,midg; midg,igrid,midg -7.7454816E-03 -1.3355885E-04 1,midg,midg; igrid,midg,midg 1.8285096E-02 1.1653493E-02 gauss-seidel spectral radius is 0.9985840 estimated iterations to convergence 211 setup time was (sec) 0.7900000 now iterating at: 19:40:20 rms-change max change #iterations 3.834296 193.8077 at 10iterations 1.774275 63.72704 at 20iterations 0.8152490 29.55145 at 30iterations 0.3792795 13.08351 at 40iterations 0.1745149 5.513122 at 50iterations 8.0697753E-02 2.566229 at 60iterations 3.7370447E-02 1.328526 at 70iterations 1.7254315E-02 0.5898557 at 80iterations 7.9825195E-03 0.2686768 at 90iterations 3.7016801E-03 0.1274559 at 100iterations 1.7059176E-03 5.2520752E-02 at 110iterations 7.9545198E-04 2.4434566E-02 at 120iterations finished qdiffx linear iterations at : 19:40:27 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 7.9545198E-04 2.4434566E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 19:40:27 7.359u 0.213s 0:08.02 94.2% 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 Mon Oct 10 2011 at 19:40:28 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2306 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: 2.831690 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): 18.91600 65.78700 ymin,ymax (A): 11.18300 55.33500 zmin,zma (A): -0.2020000 56.37200 x,y,z range (A): 46.87100 44.15200 56.57400 scale (grids/A): 2.831690 object centre (A): 42.35150 33.25900 28.08500 number of atom coordinates read : 2306 total number of charged atoms : 2171 net assigned charge : -1.999993 assigned positive charge : 333.1694 centred at (gu) : 93.66278 90.18999 84.93462 assigned negative charge : -335.1703 centred at (gu) : 93.68353 90.08557 85.17828 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 155956 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20646 grid for indexing accessible points = 1.400000 m= 77186 mr = 113699 m= 28330 mr = 62512 m= 6856 mr = 22567 m= 955 mr = 4989 m= 70 mr = 604 m= 0 mr = 29 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 64953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 17367 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) : 1.887793 object centre at (A) : 42.35150 33.25900 28.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5534718 -0.3288446 midg,1,midg; midg,igrid,midg -4.8702192E-02 -1.9860640E-02 1,midg,midg; igrid,midg,midg 0.2819643 0.1425930 gauss-seidel spectral radius is 0.9992428 estimated iterations to convergence 287 setup time was (sec) 1.490000 now iterating at: 19:40:29 rms-change max change #iterations 9.222310 296.0899 at 10iterations 5.403943 135.3959 at 20iterations 3.152280 76.64804 at 30iterations 1.831365 39.88339 at 40iterations 1.057288 28.11383 at 50iterations 0.6107323 12.33024 at 60iterations 0.3517748 7.398634 at 70iterations 0.2024505 3.858650 at 80iterations 0.1163959 2.289509 at 90iterations 6.6791937E-02 1.276686 at 100iterations 3.8279016E-02 0.7325535 at 110iterations 2.1997042E-02 0.4087124 at 120iterations 1.2608462E-02 0.2394891 at 130iterations 7.2390502E-03 0.1454821 at 140iterations 4.1557951E-03 0.1001282 at 150iterations 2.4068095E-03 4.5059204E-02 at 160iterations 1.4098621E-03 2.7887106E-02 at 170iterations 8.3955418E-04 1.8812180E-02 at 180iterations finished qdiffx linear iterations at : 19:40:39 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 8.3955418E-04 1.8812180E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 19:40:40 11.920u 0.227s 0:12.69 95.6% 0+0k 0+0io 0pf+0w