Mon Oct 10 13:59:51 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 13:59:52 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 = 4381 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5083608 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): -3.071000 66.95800 ymin,ymax (A): -12.96900 38.55500 zmin,zma (A): -20.75500 45.07500 x,y,z range (A): 70.02900 51.52400 65.83000 scale (grids/A): 0.5083608 object centre (A): 31.94350 12.79300 12.16000 number of atom coordinates read : 4381 total number of charged atoms : 4226 net assigned charge : -6.499952 assigned positive charge : 660.3458 centred at (gu) : 88.26765 89.98031 90.97247 assigned negative charge : -666.8482 centred at (gu) : 88.31158 90.09145 90.96385 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7079 nv = 96 ne = 84 npr = 91418 no. pairs analyzed = 91418 no. exposed pairs = 5073 no. arc points = 33730 no. surface atoms = 1732 nbur = 2649 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 218 mr = 3919 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3444 ## 502 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.0872996E-11 -8.4856309E-11 midg,1,midg; midg,igrid,midg 1.5564344E-10 -3.3041136E-10 1,midg,midg; igrid,midg,midg 1.9706086E-11 -1.1574905E-10 gauss-seidel spectral radius is 0.9801735 estimated iterations to convergence 59 setup time was (sec) 0.6400000 now iterating at: 13:59:52 rms-change max change #iterations 6.2880099E-02 10.68675 at 10iterations 3.8313696E-03 0.5787945 at 20iterations 4.6677206E-04 6.9015503E-02 at 30iterations 1.1442981E-04 1.2822866E-02 at 40iterations 3.1888139E-05 4.1010380E-03 at 50iterations finished qdiffx linear iterations at : 13:59:55 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 3.1888139E-05 4.1010380E-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) 3.230000 DelPhi exited at 13:59:56 3.236u 0.131s 0:04.18 80.3% 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 13:59:56 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 = 4381 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.525082 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): -3.071000 66.95800 ymin,ymax (A): -12.96900 38.55500 zmin,zma (A): -20.75500 45.07500 x,y,z range (A): 70.02900 51.52400 65.83000 scale (grids/A): 1.525082 object centre (A): 31.94350 12.79300 12.16000 number of atom coordinates read : 4381 total number of charged atoms : 4226 net assigned charge : -6.499952 assigned positive charge : 660.3458 centred at (gu) : 84.80186 89.93995 92.91608 assigned negative charge : -666.8482 centred at (gu) : 84.93420 90.27404 92.89110 start vw surface at 0.2700000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 80913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33730 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 24318 mr = 58076 m= 2121 mr = 16935 m= 34 mr = 922 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 514 time to turn everything in is 0.6400000 number of dielectric boundary points 31453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 484 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 31809 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) : 0.5083608 object centre at (A) : 31.94350 12.79300 12.16000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1887681E-02 -9.8607196E-03 midg,1,midg; midg,igrid,midg 2.4661198E-03 -1.0457372E-02 1,midg,midg; igrid,midg,midg 9.6338252E-03 -6.6733398E-03 gauss-seidel spectral radius is 0.9980350 estimated iterations to convergence 179 setup time was (sec) 0.9200000 now iterating at: 13:59:57 rms-change max change #iterations 3.589205 166.1354 at 10iterations 1.435407 45.75668 at 20iterations 0.5798808 20.48546 at 30iterations 0.2336051 7.439348 at 40iterations 9.4346210E-02 3.091640 at 50iterations 3.8216200E-02 1.393159 at 60iterations 1.5559985E-02 0.6335049 at 70iterations 6.3558514E-03 0.2253366 at 80iterations 2.6574240E-03 9.7991943E-02 at 90iterations 1.1601644E-03 3.5949707E-02 at 100iterations 5.4288632E-04 1.8631577E-02 at 110iterations 2.8237901E-04 1.0075569E-02 at 120iterations finished qdiffx linear iterations at : 14:00:03 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 2.8237901E-04 1.0075569E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 14:00:03 6.994u 0.149s 0:07.66 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 Mon Oct 10 2011 at 14:00:04 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 = 4381 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.287624 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): -3.071000 66.95800 ymin,ymax (A): -12.96900 38.55500 zmin,zma (A): -20.75500 45.07500 x,y,z range (A): 70.02900 51.52400 65.83000 scale (grids/A): 2.287624 object centre (A): 31.94350 12.79300 12.16000 number of atom coordinates read : 4381 total number of charged atoms : 4226 net assigned charge : -6.499952 assigned positive charge : 660.3458 centred at (gu) : 82.20257 89.90972 94.37366 assigned negative charge : -666.8482 centred at (gu) : 82.40129 90.41077 94.33645 start vw surface at 0.2000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 189213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33730 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 87072 mr = 142424 m= 22264 mr = 69852 m= 3128 mr = 16529 m= 111 mr = 1889 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 1770 time to turn everything in is 1.310000 number of dielectric boundary points 71083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 33695 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) : 1.525082 object centre at (A) : 31.94350 12.79300 12.16000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3724931 -0.2092963 midg,1,midg; midg,igrid,midg 2.8225724E-02 -0.1703919 1,midg,midg; igrid,midg,midg 0.2707905 -0.5141252 gauss-seidel spectral radius is 0.9991169 estimated iterations to convergence 266 setup time was (sec) 1.600000 now iterating at: 14:00:05 rms-change max change #iterations 9.663289 293.1772 at 10iterations 5.412638 154.5939 at 20iterations 3.017341 70.72437 at 30iterations 1.674461 34.59062 at 40iterations 0.9258331 18.09591 at 50iterations 0.5093776 10.32592 at 60iterations 0.2803545 5.311637 at 70iterations 0.1538719 2.960514 at 80iterations 8.4527709E-02 1.539001 at 90iterations 4.6378843E-02 0.8722343 at 100iterations 2.5399471E-02 0.4977007 at 110iterations 1.3949406E-02 0.2633495 at 120iterations 7.6735658E-03 0.1626167 at 130iterations 4.2450577E-03 7.7588558E-02 at 140iterations 2.3736779E-03 4.6088219E-02 at 150iterations 1.3431309E-03 2.5604248E-02 at 160iterations 7.8608381E-04 1.5708923E-02 at 170iterations 4.7684764E-04 1.0131836E-02 at 180iterations finished qdiffx linear iterations at : 14:00:15 total time elapsed so far: 10.97000 # loops : 180 mean,max change (kT/e) : 4.7684764E-04 1.0131836E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.14000 DelPhi exited at 14:00:15 11.147u 0.186s 0:12.05 93.9% 0+0k 0+0io 0pf+0w