Tue Oct 11 08:31:02 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 08:31:02 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3979 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 233 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5288804 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): -15.96000 51.35200 ymin,ymax (A): 24.09100 87.86600 zmin,zma (A): 15.30000 76.75500 x,y,z range (A): 67.31200 63.77501 61.45500 scale (grids/A): 0.5288804 object centre (A): 17.69600 55.97850 46.02750 number of atom coordinates read : 3979 total number of charged atoms : 3818 net assigned charge : 9.539010 assigned positive charge : 614.0794 centred at (gu) : 89.63230 90.00200 93.24226 assigned negative charge : -604.5443 centred at (gu) : 89.69641 89.95587 93.34191 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7162 nv = 96 ne = 84 npr = 77137 no. pairs analyzed = 77137 no. exposed pairs = 5516 no. arc points = 38988 no. surface atoms = 1821 nbur = 2158 mkacc time = 0.2100000 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 = 1.624000 m= 244 mr = 3391 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3875 ## 563 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3914199E-10 -3.9241088E-10 midg,1,midg; midg,igrid,midg 9.5951642E-11 5.2057930E-10 1,midg,midg; igrid,midg,midg 6.6072064E-10 1.2166516E-11 gauss-seidel spectral radius is 0.9816604 estimated iterations to convergence 61 setup time was (sec) 0.7600000 now iterating at: 08:31:03 rms-change max change #iterations 7.3353216E-02 11.07155 at 10iterations 4.7453940E-03 0.7824268 at 20iterations 4.4180060E-04 5.9503555E-02 at 30iterations 8.9257941E-05 1.0635376E-02 at 40iterations 2.3098257E-05 2.9506683E-03 at 50iterations finished qdiffx linear iterations at : 08:31:08 total time elapsed so far: 5.760000 # loops : 50 mean,max change (kT/e) : 2.3098257E-05 2.9506683E-03 energy calculations done at 5.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.940000 DelPhi exited at 08:31:09 5.946u 0.413s 0:06.67 95.2% 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 08:31:09 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3979 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 233 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.586641 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): -15.96000 51.35200 ymin,ymax (A): 24.09100 87.86600 zmin,zma (A): 15.30000 76.75500 x,y,z range (A): 67.31200 63.77501 61.45500 scale (grids/A): 1.586641 object centre (A): 17.69600 55.97850 46.02750 number of atom coordinates read : 3979 total number of charged atoms : 3818 net assigned charge : 9.539010 assigned positive charge : 614.0794 centred at (gu) : 88.89529 90.00426 99.72497 assigned negative charge : -604.5443 centred at (gu) : 89.08856 89.86736 100.0255 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38988 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22150 mr = 50907 m= 1890 mr = 13964 m= 38 mr = 727 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 434 time to turn everything in is 0.6800000 number of dielectric boundary points 37546 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 501 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 28941 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) : 0.5288804 object centre at (A) : 17.69600 55.97850 46.02750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0932118E-02 8.7554259E-03 midg,1,midg; midg,igrid,midg 1.3419506E-02 1.5046530E-02 1,midg,midg; igrid,midg,midg 2.7766215E-02 9.2895087E-03 gauss-seidel spectral radius is 0.9981726 estimated iterations to convergence 186 setup time was (sec) 1.020000 now iterating at: 08:31:10 rms-change max change #iterations 3.726519 164.8775 at 10iterations 1.546845 58.36689 at 20iterations 0.6407868 22.37639 at 30iterations 0.2654725 9.238655 at 40iterations 0.1100810 3.632420 at 50iterations 4.5733355E-02 1.617952 at 60iterations 1.9100163E-02 0.5969200 at 70iterations 7.9588536E-03 0.2995682 at 80iterations 3.3348296E-03 0.1234283 at 90iterations 1.4082439E-03 4.4498444E-02 at 100iterations 6.0656411E-04 2.5197029E-02 at 110iterations 2.6827041E-04 9.2439651E-03 at 120iterations finished qdiffx linear iterations at : 08:31:23 total time elapsed so far: 13.78000 # loops : 120 mean,max change (kT/e) : 2.6827041E-04 9.2439651E-03 energy calculations done at 13.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 08:31:24 13.947u 0.509s 0:14.83 97.3% 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 Tue Oct 11 2011 at 08:31:24 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3979 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 233 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.379962 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): -15.96000 51.35200 ymin,ymax (A): 24.09100 87.86600 zmin,zma (A): 15.30000 76.75500 x,y,z range (A): 67.31200 63.77501 61.45500 scale (grids/A): 2.379962 object centre (A): 17.69600 55.97850 46.02750 number of atom coordinates read : 3979 total number of charged atoms : 3818 net assigned charge : 9.539010 assigned positive charge : 614.0794 centred at (gu) : 88.34241 90.00604 104.5872 assigned negative charge : -604.5443 centred at (gu) : 88.63264 89.80081 105.0381 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 183686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38988 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 79036 mr = 125899 m= 19756 mr = 59274 m= 2740 mr = 13686 m= 107 mr = 1580 m= 0 mr = 20 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1494 time to turn everything in is 1.690000 number of dielectric boundary points 84866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 30504 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) : 1.586641 object centre at (A) : 17.69600 55.97850 46.02750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1173501 0.1692249 midg,1,midg; midg,igrid,midg 0.2171220 0.2722916 1,midg,midg; igrid,midg,midg 0.3612414 8.9788668E-02 gauss-seidel spectral radius is 0.9991561 estimated iterations to convergence 272 setup time was (sec) 2.100000 now iterating at: 08:31:26 rms-change max change #iterations 9.945207 310.7298 at 10iterations 5.660682 144.6262 at 20iterations 3.202428 69.26604 at 30iterations 1.797315 44.49821 at 40iterations 1.006734 23.44894 at 50iterations 0.5622249 13.00701 at 60iterations 0.3130833 6.146209 at 70iterations 0.1742781 3.724232 at 80iterations 9.6670121E-02 1.989569 at 90iterations 5.3748548E-02 1.161121 at 100iterations 2.9774468E-02 0.6060333 at 110iterations 1.6511299E-02 0.3289208 at 120iterations 9.1595445E-03 0.1945329 at 130iterations 5.0775693E-03 0.1005344 at 140iterations 2.8123711E-03 5.4228544E-02 at 150iterations 1.5675640E-03 3.2394409E-02 at 160iterations 8.7309704E-04 1.8215179E-02 at 170iterations 4.8908638E-04 1.0050774E-02 at 180iterations finished qdiffx linear iterations at : 08:31:47 total time elapsed so far: 22.98000 # loops : 180 mean,max change (kT/e) : 4.8908638E-04 1.0050774E-02 energy calculations done at 22.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.15000 DelPhi exited at 08:31:48 23.154u 0.504s 0:24.02 98.4% 0+0k 0+0io 0pf+0w