Tue Oct 11 03:49:34 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 Tue Oct 11 2011 at 03:49:34 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 70 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6604946 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): -11.77200 37.08900 ymin,ymax (A): -25.99000 22.28900 zmin,zma (A): -8.441999 45.45700 x,y,z range (A): 48.86100 48.27900 53.89900 scale (grids/A): 0.6604946 object centre (A): 12.65850 -1.850500 18.50750 number of atom coordinates read : 2703 total number of charged atoms : 2555 net assigned charge : 4.514013 assigned positive charge : 411.6979 centred at (gu) : 90.29990 90.24112 91.45019 assigned negative charge : -407.1843 centred at (gu) : 90.06042 90.07774 91.43037 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 7865 nv = 96 ne = 84 npr = 55809 no. pairs analyzed = 55809 no. exposed pairs = 3324 no. arc points = 23252 no. surface atoms = 1108 nbur = 1595 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 4410 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.4300000 number of dielectric boundary points 3856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2274 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9365 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4573541E-09 2.0907398E-08 midg,1,midg; midg,igrid,midg -2.2310038E-08 4.7407877E-08 1,midg,midg; igrid,midg,midg -3.7668844E-08 6.4306917E-08 gauss-seidel spectral radius is 0.9881261 estimated iterations to convergence 75 setup time was (sec) 0.7200000 now iterating at: 03:49:35 rms-change max change #iterations 0.1739206 21.36753 at 10iterations 1.9069254E-02 2.355727 at 20iterations 2.1001340E-03 0.2799139 at 30iterations 2.7573900E-04 3.8711548E-02 at 40iterations 5.2462008E-05 7.7133179E-03 at 50iterations finished qdiffx linear iterations at : 03:49:39 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 5.2462008E-05 7.7133179E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 03:49:39 4.304u 0.190s 0:04.77 94.1% 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 Tue Oct 11 2011 at 03:49:39 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 70 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.981484 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): -11.77200 37.08900 ymin,ymax (A): -25.99000 22.28900 zmin,zma (A): -8.441999 45.45700 x,y,z range (A): 48.86100 48.27900 53.89900 scale (grids/A): 1.981484 object centre (A): 12.65850 -1.850500 18.50750 number of atom coordinates read : 2703 total number of charged atoms : 2555 net assigned charge : 4.514013 assigned positive charge : 411.6979 centred at (gu) : 90.89889 90.72305 94.35007 assigned negative charge : -407.1843 centred at (gu) : 90.18094 90.23295 94.29082 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 84748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23252 grid for indexing accessible points = 1.400000 m= 31259 mr = 59612 m= 5073 mr = 23173 m= 337 mr = 3156 m= 5 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 484 time to turn everything in is 0.7900000 number of dielectric boundary points 35365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 20181 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) : 0.6604946 object centre at (A) : 12.65850 -1.850500 18.50750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5678382E-02 1.2568035E-02 midg,1,midg; midg,igrid,midg -1.3816183E-02 3.3834826E-02 1,midg,midg; igrid,midg,midg -9.3256356E-03 7.5191118E-02 gauss-seidel spectral radius is 0.9987456 estimated iterations to convergence 224 setup time was (sec) 1.170000 now iterating at: 03:49:41 rms-change max change #iterations 4.715703 191.9192 at 10iterations 2.294268 67.64790 at 20iterations 1.109236 33.57485 at 30iterations 0.5346943 18.81980 at 40iterations 0.2600482 7.526093 at 50iterations 0.1255980 3.826637 at 60iterations 6.0808126E-02 1.841963 at 70iterations 2.9459219E-02 0.8489609 at 80iterations 1.4280203E-02 0.4378195 at 90iterations 6.9500068E-03 0.2029028 at 100iterations 3.3907434E-03 9.3887329E-02 at 110iterations 1.6571011E-03 4.8896790E-02 at 120iterations finished qdiffx linear iterations at : 03:49:49 total time elapsed so far: 9.500000 # loops : 120 mean,max change (kT/e) : 1.6571011E-03 4.8896790E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 03:49:49 9.738u 0.222s 0:10.31 96.5% 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 Oct 11 2011 at 03:49:50 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 70 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.972226 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): -11.77200 37.08900 ymin,ymax (A): -25.99000 22.28900 zmin,zma (A): -8.441999 45.45700 x,y,z range (A): 48.86100 48.27900 53.89900 scale (grids/A): 2.972226 object centre (A): 12.65850 -1.850500 18.50750 number of atom coordinates read : 2703 total number of charged atoms : 2555 net assigned charge : 4.514013 assigned positive charge : 411.6979 centred at (gu) : 91.34832 91.08449 96.52493 assigned negative charge : -407.1843 centred at (gu) : 90.27135 90.34936 96.43606 start vw surface at 0.2100000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 195670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23252 grid for indexing accessible points = 1.400000 m= 100934 mr = 144048 m= 36947 mr = 83117 m= 9178 mr = 29509 m= 1376 mr = 6817 m= 94 mr = 930 m= 0 mr = 33 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 1673 time to turn everything in is 2.030000 number of dielectric boundary points 79745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 20440 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) : 1.981484 object centre at (A) : 12.65850 -1.850500 18.50750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3965910 0.2924353 midg,1,midg; midg,igrid,midg -0.1653522 0.3825769 1,midg,midg; igrid,midg,midg -5.7574902E-02 0.6200832 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 2.420000 now iterating at: 03:49:52 rms-change max change #iterations 10.84485 358.8105 at 10iterations 6.371839 158.0481 at 20iterations 3.738863 73.74025 at 30iterations 2.187104 44.62188 at 40iterations 1.276780 31.45881 at 50iterations 0.7479880 13.61619 at 60iterations 0.4355520 7.241005 at 70iterations 0.2543097 4.721115 at 80iterations 0.1477777 2.703270 at 90iterations 8.6152494E-02 1.582942 at 100iterations 5.0215043E-02 0.8624172 at 110iterations 2.9262263E-02 0.6154269 at 120iterations 1.7023275E-02 0.2916200 at 130iterations 9.9712787E-03 0.1614189 at 140iterations 5.8285524E-03 9.9426270E-02 at 150iterations 3.4354597E-03 5.8940887E-02 at 160iterations 2.0467760E-03 3.6237001E-02 at 170iterations 1.2340082E-03 2.3178101E-02 at 180iterations finished qdiffx linear iterations at : 03:50:05 total time elapsed so far: 15.48000 # loops : 180 mean,max change (kT/e) : 1.2340082E-03 2.3178101E-02 energy calculations done at 15.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.71000 DelPhi exited at 03:50:06 15.710u 0.201s 0:16.24 97.9% 0+0k 0+0io 0pf+0w