Mon Oct 10 19:35:52 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 Mon Oct 10 2011 at 19:35:52 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: GLM 31 has a net charge of -0.0940 !!! WARNING: ASL 108 has a net charge of -0.1000 !!! WARNING: GLM 111 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5326551 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): -8.450000 39.19100 ymin,ymax (A): -5.798000 45.38100 zmin,zma (A): -11.76000 55.07500 x,y,z range (A): 47.64100 51.17900 66.83500 scale (grids/A): 0.5326551 object centre (A): 15.37050 19.79150 21.65750 number of atom coordinates read : 2731 total number of charged atoms : 2583 net assigned charge : 1.712031 assigned positive charge : 402.8306 centred at (gu) : 90.62553 90.62984 91.04427 assigned negative charge : -401.1195 centred at (gu) : 90.54935 90.68491 90.94268 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5207 nv = 96 ne = 84 npr = 52601 no. pairs analyzed = 52601 no. exposed pairs = 3900 no. arc points = 26945 no. surface atoms = 1299 nbur = 1432 mkacc time = 0.1400000 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 = 1.596000 m= 217 mr = 2474 m= 0 mr = 13 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2679 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3813052E-10 5.4710630E-10 midg,1,midg; midg,igrid,midg 2.1682189E-10 -1.6692998E-10 1,midg,midg; igrid,midg,midg -1.8567629E-10 3.8612408E-10 gauss-seidel spectral radius is 0.9818297 estimated iterations to convergence 61 setup time was (sec) 0.5900000 now iterating at: 19:35:53 rms-change max change #iterations 6.2009189E-02 12.67847 at 10iterations 4.0000225E-03 0.7666092 at 20iterations 2.9084762E-04 5.0114989E-02 at 30iterations 3.5752968E-05 5.1212311E-03 at 40iterations 6.7407650E-06 9.6273422E-04 at 50iterations finished qdiffx linear iterations at : 19:35:57 total time elapsed so far: 4.950000 # loops : 50 mean,max change (kT/e) : 6.7407650E-06 9.6273422E-04 energy calculations done at 4.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.120000 DelPhi exited at 19:35:58 5.124u 0.405s 0:05.99 92.1% 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 Mon Oct 10 2011 at 19:35:58 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: GLM 31 has a net charge of -0.0940 !!! WARNING: ASL 108 has a net charge of -0.1000 !!! WARNING: GLM 111 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.597965 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): -8.450000 39.19100 ymin,ymax (A): -5.798000 45.38100 zmin,zma (A): -11.76000 55.07500 x,y,z range (A): 47.64100 51.17900 66.83500 scale (grids/A): 1.597965 object centre (A): 15.37050 19.79150 21.65750 number of atom coordinates read : 2731 total number of charged atoms : 2583 net assigned charge : 1.712031 assigned positive charge : 402.8306 centred at (gu) : 91.87581 91.88894 93.13184 assigned negative charge : -401.1195 centred at (gu) : 91.64814 92.05453 92.82787 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 56934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26945 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18109 mr = 36759 m= 1924 mr = 12021 m= 45 mr = 897 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 175 time to turn everything in is 0.4800000 number of dielectric boundary points 27335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 304 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 19678 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) : 0.5326551 object centre at (A) : 15.37050 19.79150 21.65750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9738101E-03 1.8855061E-02 midg,1,midg; midg,igrid,midg -2.6038720E-03 -6.4677321E-03 1,midg,midg; igrid,midg,midg -4.8961118E-04 1.5706802E-04 gauss-seidel spectral radius is 0.9980894 estimated iterations to convergence 182 setup time was (sec) 0.7800000 now iterating at: 19:36:02 rms-change max change #iterations 3.018963 143.0702 at 10iterations 1.230662 49.94056 at 20iterations 0.5024254 21.66318 at 30iterations 0.2042871 7.739687 at 40iterations 8.3067432E-02 3.238846 at 50iterations 3.3841707E-02 1.369904 at 60iterations 1.3853922E-02 0.5319805 at 70iterations 5.6428327E-03 0.2355616 at 80iterations 2.3134898E-03 8.3402634E-02 at 90iterations 9.4786251E-04 4.1061401E-02 at 100iterations 3.8670487E-04 1.5181541E-02 at 110iterations 1.5945736E-04 6.6804886E-03 at 120iterations finished qdiffx linear iterations at : 19:36:12 total time elapsed so far: 11.14000 # loops : 120 mean,max change (kT/e) : 1.5945736E-04 6.6804886E-03 energy calculations done at 11.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 19:36:13 11.318u 0.480s 0:14.84 79.4% 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 19:36:13 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: GLM 31 has a net charge of -0.0940 !!! WARNING: ASL 108 has a net charge of -0.1000 !!! WARNING: GLM 111 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.396948 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): -8.450000 39.19100 ymin,ymax (A): -5.798000 45.38100 zmin,zma (A): -11.76000 55.07500 x,y,z range (A): 47.64100 51.17900 66.83500 scale (grids/A): 2.396948 object centre (A): 15.37050 19.79150 21.65750 number of atom coordinates read : 2731 total number of charged atoms : 2583 net assigned charge : 1.712031 assigned positive charge : 402.8306 centred at (gu) : 92.81367 92.83324 94.69761 assigned negative charge : -401.1195 centred at (gu) : 92.47214 93.08164 94.24180 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 132161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26945 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 60982 mr = 90612 m= 18226 mr = 46803 m= 2881 mr = 13358 m= 181 mr = 1809 m= 7 mr = 77 m= 0 mr = 1 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 698 time to turn everything in is 1.180000 number of dielectric boundary points 61778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 20639 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) : 1.597965 object centre at (A) : 15.37050 19.79150 21.65750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3776208 0.2307583 midg,1,midg; midg,igrid,midg -4.7652643E-02 -6.7901351E-02 1,midg,midg; igrid,midg,midg 2.0926916E-03 -1.7598629E-02 gauss-seidel spectral radius is 0.9991133 estimated iterations to convergence 265 setup time was (sec) 1.510000 now iterating at: 19:36:15 rms-change max change #iterations 7.927309 267.1575 at 10iterations 4.436013 138.0020 at 20iterations 2.455137 68.74841 at 30iterations 1.356661 31.03750 at 40iterations 0.7461876 19.02385 at 50iterations 0.4095197 11.70455 at 60iterations 0.2245412 5.578459 at 70iterations 0.1225774 2.979172 at 80iterations 6.6934764E-02 1.535812 at 90iterations 3.6519278E-02 0.8062419 at 100iterations 1.9946815E-02 0.4631805 at 110iterations 1.0908891E-02 0.2588558 at 120iterations 5.9392718E-03 0.1330128 at 130iterations 3.2370405E-03 7.2048187E-02 at 140iterations 1.7622696E-03 3.8025856E-02 at 150iterations 9.5945224E-04 2.2065520E-02 at 160iterations 5.2231812E-04 1.1060238E-02 at 170iterations 2.8491046E-04 6.1821938E-03 at 180iterations finished qdiffx linear iterations at : 19:36:31 total time elapsed so far: 18.36000 # loops : 180 mean,max change (kT/e) : 2.8491046E-04 6.1821938E-03 energy calculations done at 18.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.52000 DelPhi exited at 19:36:32 18.529u 0.462s 0:19.47 97.4% 0+0k 0+0io 0pf+0w