Tue Oct 11 06:18:00 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 06:18:00 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2033 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7090504 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): 27.95300 71.60700 ymin,ymax (A): 43.71600 81.07200 zmin,zma (A): -60.31200 -10.10400 x,y,z range (A): 43.65400 37.35600 50.20800 scale (grids/A): 0.7090504 object centre (A): 49.78000 62.39400 -35.20800 number of atom coordinates read : 2033 total number of charged atoms : 1903 net assigned charge : 7.025010 assigned positive charge : 308.9221 centred at (gu) : 90.05230 89.77928 89.12995 assigned negative charge : -301.8972 centred at (gu) : 90.21944 89.80621 89.13179 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6988 nv = 96 ne = 84 npr = 40414 no. pairs analyzed = 40414 no. exposed pairs = 2615 no. arc points = 17765 no. surface atoms = 878 nbur = 1155 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 477 mr = 3882 m= 4 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1589 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3687083E-08 5.1622315E-08 midg,1,midg; midg,igrid,midg 7.8139642E-08 4.6317869E-08 1,midg,midg; igrid,midg,midg 1.4167472E-07 -2.2916458E-08 gauss-seidel spectral radius is 0.9896289 estimated iterations to convergence 80 setup time was (sec) 0.5500000 now iterating at: 06:18:01 rms-change max change #iterations 0.1994296 34.22903 at 10iterations 2.5087396E-02 3.978467 at 20iterations 3.3907660E-03 0.5025005 at 30iterations 5.8685307E-04 7.4440002E-02 at 40iterations 1.4631935E-04 1.8661499E-02 at 50iterations finished qdiffx linear iterations at : 06:18:05 total time elapsed so far: 4.770000 # loops : 50 mean,max change (kT/e) : 1.4631935E-04 1.8661499E-02 energy calculations done at 4.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.940000 DelPhi exited at 06:18:06 4.945u 0.449s 0:05.78 93.0% 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 06:18:06 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2033 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.127151 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): 27.95300 71.60700 ymin,ymax (A): 43.71600 81.07200 zmin,zma (A): -60.31200 -10.10400 x,y,z range (A): 43.65400 37.35600 50.20800 scale (grids/A): 2.127151 object centre (A): 49.78000 62.39400 -35.20800 number of atom coordinates read : 2033 total number of charged atoms : 1903 net assigned charge : 7.025010 assigned positive charge : 308.9221 centred at (gu) : 90.15693 89.33796 87.38979 assigned negative charge : -301.8972 centred at (gu) : 90.65859 89.41888 87.39536 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17765 grid for indexing accessible points = 1.400000 m= 30560 mr = 51988 m= 5929 mr = 22997 m= 519 mr = 3858 m= 16 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 32022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15112 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) : 0.7090504 object centre at (A) : 49.78000 62.39400 -35.20800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1088164E-02 2.8648458E-03 midg,1,midg; midg,igrid,midg 3.0833367E-02 1.2175370E-02 1,midg,midg; igrid,midg,midg 4.6550650E-02 1.8242165E-02 gauss-seidel spectral radius is 0.9988357 estimated iterations to convergence 232 setup time was (sec) 0.9800000 now iterating at: 06:18:07 rms-change max change #iterations 4.587292 193.4569 at 10iterations 2.279633 71.63409 at 20iterations 1.131574 42.44349 at 30iterations 0.5602816 18.94511 at 40iterations 0.2789809 9.473763 at 50iterations 0.1385883 4.200440 at 60iterations 6.9356687E-02 2.127449 at 70iterations 3.4426972E-02 1.005696 at 80iterations 1.7228164E-02 0.4963188 at 90iterations 8.6226445E-03 0.2496619 at 100iterations 4.3417043E-03 0.1390371 at 110iterations 2.2384641E-03 6.8378448E-02 at 120iterations finished qdiffx linear iterations at : 06:18:19 total time elapsed so far: 11.98000 # loops : 120 mean,max change (kT/e) : 2.2384641E-03 6.8378448E-02 energy calculations done at 11.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 06:18:19 12.162u 0.492s 0:12.97 97.5% 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 06:18:19 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2033 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.190727 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): 27.95300 71.60700 ymin,ymax (A): 43.71600 81.07200 zmin,zma (A): -60.31200 -10.10400 x,y,z range (A): 43.65400 37.35600 50.20800 scale (grids/A): 3.190727 object centre (A): 49.78000 62.39400 -35.20800 number of atom coordinates read : 2033 total number of charged atoms : 1903 net assigned charge : 7.025010 assigned positive charge : 308.9221 centred at (gu) : 90.23531 89.00690 86.08476 assigned negative charge : -301.8972 centred at (gu) : 90.98779 89.12844 86.09306 start vw surface at 0.1200000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 170529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17765 grid for indexing accessible points = 1.400000 m= 94265 mr = 125387 m= 39122 mr = 78053 m= 11183 mr = 31823 m= 2079 mr = 8438 m= 210 mr = 1423 m= 3 mr = 83 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.040000 number of dielectric boundary points 72185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 15220 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) : 2.127151 object centre at (A) : 49.78000 62.39400 -35.20800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2581021 -0.1279200 midg,1,midg; midg,igrid,midg 0.2436361 9.0917088E-02 1,midg,midg; igrid,midg,midg 0.3952955 0.2928722 gauss-seidel spectral radius is 0.9992968 estimated iterations to convergence 298 setup time was (sec) 2.420000 now iterating at: 06:18:22 rms-change max change #iterations 10.25359 343.5493 at 10iterations 6.109903 136.6470 at 20iterations 3.628831 78.71935 at 30iterations 2.151820 46.58417 at 40iterations 1.272816 23.10466 at 50iterations 0.7478493 15.13837 at 60iterations 0.4404249 7.845370 at 70iterations 0.2599325 4.821326 at 80iterations 0.1524269 2.892731 at 90iterations 8.9678027E-02 1.571533 at 100iterations 5.2555095E-02 0.9626694 at 110iterations 3.0995360E-02 0.5498998 at 120iterations 1.8329477E-02 0.3385963 at 130iterations 1.1005921E-02 0.2014351 at 140iterations 6.6969665E-03 0.1244011 at 150iterations 4.2033200E-03 8.0907822E-02 at 160iterations 2.7706935E-03 5.3386688E-02 at 170iterations 1.9363450E-03 3.2367706E-02 at 180iterations finished qdiffx linear iterations at : 06:18:41 total time elapsed so far: 21.10000 # loops : 180 mean,max change (kT/e) : 1.9363450E-03 3.2367706E-02 energy calculations done at 21.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.27000 DelPhi exited at 06:18:41 21.278u 0.509s 0:22.10 98.5% 0+0k 0+0io 0pf+0w