Wed Dec 28 11:01:09 PST 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 Wed Dec 28 2011 at 11:01:09 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6313512 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): -10.95600 35.27600 ymin,ymax (A): 1.601000 41.29000 zmin,zma (A): -19.33100 37.05600 x,y,z range (A): 46.23200 39.68900 56.38700 scale (grids/A): 0.6313512 object centre (A): 12.16000 21.44550 8.862500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 89.86211 89.53460 89.97847 assigned negative charge : -285.8263 centred at (gu) : 89.95376 89.68626 89.95988 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5389 nv = 96 ne = 84 npr = 40059 no. pairs analyzed = 40059 no. exposed pairs = 2399 no. arc points = 16715 no. surface atoms = 819 nbur = 1145 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 297 mr = 3089 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1682 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6295 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5626584E-10 3.4528664E-09 midg,1,midg; midg,igrid,midg 1.3633809E-08 -7.4146760E-09 1,midg,midg; igrid,midg,midg 8.6101277E-09 -3.9292756E-09 gauss-seidel spectral radius is 0.9869485 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 11:01:10 rms-change max change #iterations 0.1166033 19.82295 at 10iterations 1.1017153E-02 2.195588 at 20iterations 1.0657655E-03 0.1718426 at 30iterations 1.0271651E-04 1.7364502E-02 at 40iterations 9.6047161E-06 1.3971329E-03 at 50iterations finished qdiffx linear iterations at : 11:01:13 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 9.6047161E-06 1.3971329E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 11:01:14 3.706u 0.406s 0:04.66 87.9% 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 Wed Dec 28 2011 at 11:01:14 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.894054 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): -10.95600 35.27600 ymin,ymax (A): 1.601000 41.29000 zmin,zma (A): -19.33100 37.05600 x,y,z range (A): 46.23200 39.68900 56.38700 scale (grids/A): 1.894054 object centre (A): 12.16000 21.44550 8.862500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 89.58641 88.60387 89.93537 assigned negative charge : -285.8263 centred at (gu) : 89.86156 89.05893 89.87996 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 57868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16715 grid for indexing accessible points = 1.400000 m= 22193 mr = 40457 m= 3701 mr = 17335 m= 204 mr = 2542 m= 1 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 866 time to turn everything in is 0.4700000 number of dielectric boundary points 23555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14407 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) : 0.6313512 object centre at (A) : 12.16000 21.44550 8.862500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3566590E-02 3.4490157E-02 midg,1,midg; midg,igrid,midg 3.8377817E-03 -1.1476776E-02 1,midg,midg; igrid,midg,midg -2.6084702E-03 -5.2941623E-03 gauss-seidel spectral radius is 0.9985445 estimated iterations to convergence 208 setup time was (sec) 0.7500000 now iterating at: 11:01:15 rms-change max change #iterations 3.524508 169.7665 at 10iterations 1.611204 67.09800 at 20iterations 0.7383050 26.43879 at 30iterations 0.3372360 12.46304 at 40iterations 0.1538937 5.410351 at 50iterations 7.0264220E-02 2.441338 at 60iterations 3.2077208E-02 1.176140 at 70iterations 1.4699752E-02 0.5027771 at 80iterations 6.7013744E-03 0.2439871 at 90iterations 3.0668369E-03 0.1193085 at 100iterations 1.3973557E-03 4.6480894E-02 at 110iterations 6.4046663E-04 2.2102833E-02 at 120iterations finished qdiffx linear iterations at : 11:01:24 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 6.4046663E-04 2.2102833E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 11:01:25 9.449u 0.473s 0:10.77 92.0% 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 Wed Dec 28 2011 at 11:01:25 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.841080 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): -10.95600 35.27600 ymin,ymax (A): 1.601000 41.29000 zmin,zma (A): -19.33100 37.05600 x,y,z range (A): 46.23200 39.68900 56.38700 scale (grids/A): 2.841080 object centre (A): 12.16000 21.44550 8.862500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 89.37961 87.90596 89.90303 assigned negative charge : -285.8263 centred at (gu) : 89.79230 88.58838 89.81998 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 133690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16715 grid for indexing accessible points = 1.400000 m= 70603 mr = 97770 m= 27577 mr = 59435 m= 6831 mr = 23302 m= 918 mr = 5453 m= 51 mr = 622 m= 0 mr = 24 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 2914 time to turn everything in is 1.290000 number of dielectric boundary points 53064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 14655 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) : 1.894054 object centre at (A) : 12.16000 21.44550 8.862500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3000824 0.2748067 midg,1,midg; midg,igrid,midg 8.9608930E-04 -0.1250513 1,midg,midg; igrid,midg,midg -6.1774556E-02 -7.7500559E-02 gauss-seidel spectral radius is 0.9992151 estimated iterations to convergence 282 setup time was (sec) 1.610000 now iterating at: 11:01:27 rms-change max change #iterations 8.380793 339.3828 at 10iterations 4.797070 122.6657 at 20iterations 2.728950 84.45370 at 30iterations 1.547121 39.22846 at 40iterations 0.8738590 18.72413 at 50iterations 0.4951926 10.29020 at 60iterations 0.2798213 5.393576 at 70iterations 0.1577830 3.249763 at 80iterations 8.9230247E-02 1.758483 at 90iterations 5.0415933E-02 1.002016 at 100iterations 2.8442487E-02 0.6238351 at 110iterations 1.6041854E-02 0.3334684 at 120iterations 9.0583861E-03 0.1850014 at 130iterations 5.1081814E-03 0.1097412 at 140iterations 2.8808771E-03 5.9034348E-02 at 150iterations 1.6258719E-03 3.6406755E-02 at 160iterations 9.1902446E-04 2.1652222E-02 at 170iterations 5.1781716E-04 1.1002541E-02 at 180iterations finished qdiffx linear iterations at : 11:01:48 total time elapsed so far: 22.68000 # loops : 180 mean,max change (kT/e) : 5.1781716E-04 1.1002541E-02 energy calculations done at 22.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.86000 DelPhi exited at 11:01:49 22.865u 0.590s 0:24.00 97.7% 0+0k 0+0io 0pf+0w