Tue Oct 11 03:58:37 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 Tue Oct 11 2011 at 03:58:37 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6406219 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): -11.30400 37.28100 ymin,ymax (A): -25.76200 22.35900 zmin,zma (A): -10.38700 45.18400 x,y,z range (A): 48.58500 48.12100 55.57100 scale (grids/A): 0.6406219 object centre (A): 12.98850 -1.701500 17.39850 number of atom coordinates read : 2764 total number of charged atoms : 2611 net assigned charge : 0.1400135 assigned positive charge : 415.6707 centred at (gu) : 90.13907 90.32519 91.78566 assigned negative charge : -415.5314 centred at (gu) : 89.90894 90.19797 91.72052 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7435 nv = 96 ne = 84 npr = 57231 no. pairs analyzed = 57231 no. exposed pairs = 3352 no. arc points = 23514 no. surface atoms = 1137 nbur = 1627 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 4124 m= 1 mr = 39 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 0.4000000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2371 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6567941E-09 1.2120198E-08 midg,1,midg; midg,igrid,midg -1.5231633E-08 1.7047480E-08 1,midg,midg; igrid,midg,midg -2.9009264E-08 2.9290824E-08 gauss-seidel spectral radius is 0.9873849 estimated iterations to convergence 73 setup time was (sec) 0.7400000 now iterating at: 03:58:38 rms-change max change #iterations 0.1514489 22.35173 at 10iterations 1.5222573E-02 2.279570 at 20iterations 1.5239948E-03 0.1875238 at 30iterations 1.5790247E-04 2.2688866E-02 at 40iterations 1.7899318E-05 2.7513504E-03 at 50iterations finished qdiffx linear iterations at : 03:58:41 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 1.7899318E-05 2.7513504E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 03:58:42 4.509u 0.418s 0:05.44 90.2% 0+0k 0+0io 5pf+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 03:58:42 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.921866 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): -11.30400 37.28100 ymin,ymax (A): -25.76200 22.35900 zmin,zma (A): -10.38700 45.18400 x,y,z range (A): 48.58500 48.12100 55.57100 scale (grids/A): 1.921866 object centre (A): 12.98850 -1.701500 17.39850 number of atom coordinates read : 2764 total number of charged atoms : 2611 net assigned charge : 0.1400135 assigned positive charge : 415.6707 centred at (gu) : 90.41656 90.97499 95.35628 assigned negative charge : -415.5314 centred at (gu) : 89.72690 90.59345 95.16142 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 80504 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23514 grid for indexing accessible points = 1.400000 m= 28944 mr = 56573 m= 4350 mr = 21357 m= 242 mr = 2659 m= 5 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 802 time to turn everything in is 0.8200000 number of dielectric boundary points 33381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20547 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) : 0.6406219 object centre at (A) : 12.98850 -1.701500 17.39850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1422145E-02 -2.8725753E-03 midg,1,midg; midg,igrid,midg -1.2549163E-02 2.4613362E-02 1,midg,midg; igrid,midg,midg -1.2233674E-02 5.2838728E-02 gauss-seidel spectral radius is 0.9986728 estimated iterations to convergence 217 setup time was (sec) 1.140000 now iterating at: 03:58:44 rms-change max change #iterations 4.453684 278.8789 at 10iterations 2.115079 77.33679 at 20iterations 1.002613 28.98396 at 30iterations 0.4761996 14.98333 at 40iterations 0.2254182 7.130043 at 50iterations 0.1068060 3.064607 at 60iterations 5.0623372E-02 1.620975 at 70iterations 2.4107441E-02 0.7686548 at 80iterations 1.1410629E-02 0.3386841 at 90iterations 5.4205330E-03 0.1594372 at 100iterations 2.5697737E-03 7.4819565E-02 at 110iterations 1.2189345E-03 3.6860466E-02 at 120iterations finished qdiffx linear iterations at : 03:58:53 total time elapsed so far: 10.40000 # loops : 120 mean,max change (kT/e) : 1.2189345E-03 3.6860466E-02 energy calculations done at 10.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.62000 DelPhi exited at 03:58:54 10.620u 0.455s 0:11.67 94.8% 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 Tue Oct 11 2011 at 03:58:54 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.882798 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): -11.30400 37.28100 ymin,ymax (A): -25.76200 22.35900 zmin,zma (A): -10.38700 45.18400 x,y,z range (A): 48.58500 48.12100 55.57100 scale (grids/A): 2.882798 object centre (A): 12.98850 -1.701500 17.39850 number of atom coordinates read : 2764 total number of charged atoms : 2611 net assigned charge : 0.1400135 assigned positive charge : 415.6707 centred at (gu) : 90.62479 91.46232 98.03427 assigned negative charge : -415.5314 centred at (gu) : 89.59020 90.89030 97.74211 start vw surface at 0.1600000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 186072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23514 grid for indexing accessible points = 1.400000 m= 94659 mr = 136645 m= 33648 mr = 77751 m= 7852 mr = 27075 m= 1109 mr = 5842 m= 55 mr = 711 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 2885 time to turn everything in is 2.140000 number of dielectric boundary points 75349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 20884 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) : 1.921866 object centre at (A) : 12.98850 -1.701500 17.39850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7460400 0.1932133 midg,1,midg; midg,igrid,midg -0.1489100 0.3094200 1,midg,midg; igrid,midg,midg -9.2505433E-02 0.4939455 gauss-seidel spectral radius is 0.9992671 estimated iterations to convergence 292 setup time was (sec) 2.510000 now iterating at: 03:58:57 rms-change max change #iterations 10.44162 418.6666 at 10iterations 6.132747 138.9737 at 20iterations 3.583388 72.25519 at 30iterations 2.087137 38.60815 at 40iterations 1.213469 21.96375 at 50iterations 0.7026430 13.51443 at 60iterations 0.4071952 7.407802 at 70iterations 0.2358816 4.164900 at 80iterations 0.1364252 2.448151 at 90iterations 7.8809164E-02 1.397751 at 100iterations 4.5517694E-02 0.7990036 at 110iterations 2.6324902E-02 0.4370508 at 120iterations 1.5211633E-02 0.2753963 at 130iterations 8.8019101E-03 0.1631413 at 140iterations 5.0876676E-03 9.3330383E-02 at 150iterations 2.9537454E-03 5.1452637E-02 at 160iterations 1.7150644E-03 3.2458305E-02 at 170iterations 1.0045263E-03 1.8267632E-02 at 180iterations finished qdiffx linear iterations at : 03:59:12 total time elapsed so far: 18.26000 # loops : 180 mean,max change (kT/e) : 1.0045263E-03 1.8267632E-02 energy calculations done at 18.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.47000 DelPhi exited at 03:59:13 18.478u 0.449s 0:19.32 97.8% 0+0k 0+0io 0pf+0w