Tue Oct 11 06:11:12 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 06:11:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2051 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7612856 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): -18.03600 28.26700 ymin,ymax (A): -11.63600 31.03000 zmin,zma (A): -9.033999 37.72900 x,y,z range (A): 46.30300 42.66600 46.76300 scale (grids/A): 0.7612856 object centre (A): 5.115500 9.697001 14.34750 number of atom coordinates read : 2051 total number of charged atoms : 1925 net assigned charge : 8.500011 assigned positive charge : 312.4120 centred at (gu) : 90.54489 90.01151 91.31781 assigned negative charge : -303.9122 centred at (gu) : 90.44380 89.94422 91.15015 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8147 nv = 96 ne = 84 npr = 41181 no. pairs analyzed = 41181 no. exposed pairs = 2525 no. arc points = 17005 no. surface atoms = 859 nbur = 1192 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 678 mr = 4776 m= 4 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3000000 number of dielectric boundary points 3908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1377 ## 121 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2957521E-08 6.0137819E-07 midg,1,midg; midg,igrid,midg 1.3027287E-07 3.2899587E-07 1,midg,midg; igrid,midg,midg 7.3698196E-08 4.1619273E-07 gauss-seidel spectral radius is 0.9909925 estimated iterations to convergence 86 setup time was (sec) 0.5700000 now iterating at: 06:11:13 rms-change max change #iterations 0.2675572 33.76537 at 10iterations 3.8698342E-02 4.405870 at 20iterations 5.5875201E-03 0.6175542 at 30iterations 8.7889255E-04 0.1067443 at 40iterations 1.7758604E-04 2.3271561E-02 at 50iterations finished qdiffx linear iterations at : 06:11:16 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 1.7758604E-04 2.3271561E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 06:11:16 4.026u 0.263s 0:04.58 93.4% 0+0k 0+0io 6pf+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 06:11:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2051 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.283857 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): -18.03600 28.26700 ymin,ymax (A): -11.63600 31.03000 zmin,zma (A): -9.033999 37.72900 x,y,z range (A): 46.30300 42.66600 46.76300 scale (grids/A): 2.283857 object centre (A): 5.115500 9.697001 14.34750 number of atom coordinates read : 2051 total number of charged atoms : 1925 net assigned charge : 8.500011 assigned positive charge : 312.4120 centred at (gu) : 91.63452 90.03458 93.95349 assigned negative charge : -303.9122 centred at (gu) : 91.33153 89.83269 93.45064 start vw surface at 0.1400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 85132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17005 grid for indexing accessible points = 1.400000 m= 37636 mr = 60853 m= 8948 mr = 29138 m= 1199 mr = 6305 m= 56 mr = 710 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 304 time to turn everything in is 0.8100000 number of dielectric boundary points 35959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 15351 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) : 0.7612856 object centre at (A) : 5.115500 9.697001 14.34750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2906103E-02 7.9070613E-02 midg,1,midg; midg,igrid,midg 4.0099435E-02 3.6088418E-02 1,midg,midg; igrid,midg,midg 5.7864051E-02 0.1201693 gauss-seidel spectral radius is 0.9989623 estimated iterations to convergence 246 setup time was (sec) 1.100000 now iterating at: 06:11:18 rms-change max change #iterations 5.140053 215.7205 at 10iterations 2.668225 94.74224 at 20iterations 1.378819 36.12532 at 30iterations 0.7136174 19.95514 at 40iterations 0.3696031 9.692602 at 50iterations 0.1909637 5.942986 at 60iterations 9.8789871E-02 2.722885 at 70iterations 5.1128153E-02 1.361193 at 80iterations 2.6484478E-02 0.7857571 at 90iterations 1.3702922E-02 0.4267716 at 100iterations 7.1611907E-03 0.2028418 at 110iterations 3.7555681E-03 0.1112823 at 120iterations finished qdiffx linear iterations at : 06:11:26 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 3.7555681E-03 0.1112823 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 06:11:27 9.673u 0.290s 0:10.47 95.1% 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 06:11:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2051 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.425785 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): -18.03600 28.26700 ymin,ymax (A): -11.63600 31.03000 zmin,zma (A): -9.033999 37.72900 x,y,z range (A): 46.30300 42.66600 46.76300 scale (grids/A): 3.425785 object centre (A): 5.115500 9.697001 14.34750 number of atom coordinates read : 2051 total number of charged atoms : 1925 net assigned charge : 8.500011 assigned positive charge : 312.4120 centred at (gu) : 92.45168 90.05176 95.93031 assigned negative charge : -303.9122 centred at (gu) : 91.99741 89.74908 95.17596 start vw surface at 0.1500000 fill in re-entrant regions at 1.160000 boundary points on vw surface= 195811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17005 grid for indexing accessible points = 1.400000 m= 112117 mr = 145933 m= 51585 mr = 94136 m= 17512 mr = 43189 m= 4511 mr = 13898 m= 853 mr = 3465 m= 64 mr = 614 m= 0 mr = 22 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 984 time to turn everything in is 2.680000 number of dielectric boundary points 81196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.840000 number of grid points assigned charge 15400 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) : 2.283857 object centre at (A) : 5.115500 9.697001 14.34750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5748577 0.6350771 midg,1,midg; midg,igrid,midg 0.2739776 0.1363047 1,midg,midg; igrid,midg,midg 0.4097675 0.8136684 gauss-seidel spectral radius is 0.9993319 estimated iterations to convergence 305 setup time was (sec) 3.010000 now iterating at: 06:11:30 rms-change max change #iterations 11.05589 386.4701 at 10iterations 6.688899 129.0453 at 20iterations 4.019246 71.55262 at 30iterations 2.405564 44.80100 at 40iterations 1.436327 24.11402 at 50iterations 0.8583742 13.94352 at 60iterations 0.5109924 8.357773 at 70iterations 0.3042577 5.121151 at 80iterations 0.1809336 2.779900 at 90iterations 0.1077288 1.801510 at 100iterations 6.4111099E-02 0.9758244 at 110iterations 3.8213912E-02 0.7090912 at 120iterations 2.2883348E-02 0.3894958 at 130iterations 1.3843681E-02 0.2275543 at 140iterations 8.5364282E-03 0.1492500 at 150iterations 5.4196827E-03 8.9345932E-02 at 160iterations 3.6139626E-03 6.1050415E-02 at 170iterations 2.5687022E-03 4.2047501E-02 at 180iterations finished qdiffx linear iterations at : 06:11:44 total time elapsed so far: 16.96000 # loops : 180 mean,max change (kT/e) : 2.5687022E-03 4.2047501E-02 energy calculations done at 16.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.14000 DelPhi exited at 06:11:45 17.141u 0.307s 0:17.83 97.8% 0+0k 0+0io 0pf+0w