Tue Oct 11 07:02:09 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 07:02:10 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 !!! WARNING: UMP 469 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5692903 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): -3.320000 59.21400 ymin,ymax (A): -41.74600 16.82700 zmin,zma (A): 5.766000 53.91700 x,y,z range (A): 62.53400 58.57300 48.15100 scale (grids/A): 0.5692903 object centre (A): 27.94700 -12.45950 29.84150 number of atom coordinates read : 3037 total number of charged atoms : 2893 net assigned charge : -4.099982 assigned positive charge : 444.8854 centred at (gu) : 91.60517 90.29381 90.44759 assigned negative charge : -448.9860 centred at (gu) : 91.45176 90.15802 90.48540 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6430 nv = 96 ne = 84 npr = 62874 no. pairs analyzed = 62874 no. exposed pairs = 3782 no. arc points = 26772 no. surface atoms = 1275 nbur = 1762 mkacc time = 0.1500000 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 = 1.512000 m= 252 mr = 3402 m= 0 mr = 19 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2710 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8298 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7959978E-11 -1.3805327E-09 midg,1,midg; midg,igrid,midg -2.5981071E-09 1.5163893E-09 1,midg,midg; igrid,midg,midg -2.0949449E-09 2.4947111E-09 gauss-seidel spectral radius is 0.9840858 estimated iterations to convergence 65 setup time was (sec) 0.5700000 now iterating at: 07:02:10 rms-change max change #iterations 9.2500716E-02 14.44192 at 10iterations 6.6800299E-03 1.052843 at 20iterations 5.0622236E-04 7.8263283E-02 at 30iterations 3.7570062E-05 6.5412521E-03 at 40iterations 3.1182469E-06 4.8446655E-04 at 50iterations finished qdiffx linear iterations at : 07:02:13 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 3.1182469E-06 4.8446655E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 07:02:14 3.596u 0.183s 0:04.06 92.8% 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 07:02:14 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 !!! WARNING: UMP 469 has a net charge of -0.1000 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: 1.707871 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): -3.320000 59.21400 ymin,ymax (A): -41.74600 16.82700 zmin,zma (A): 5.766000 53.91700 x,y,z range (A): 62.53400 58.57300 48.15100 scale (grids/A): 1.707871 object centre (A): 27.94700 -12.45950 29.84150 number of atom coordinates read : 3037 total number of charged atoms : 2893 net assigned charge : -4.099982 assigned positive charge : 444.8854 centred at (gu) : 94.81461 90.88058 91.34205 assigned negative charge : -448.9860 centred at (gu) : 94.35471 90.47356 91.45593 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 71002 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26772 grid for indexing accessible points = 1.400000 m= 22722 mr = 48520 m= 2511 mr = 16198 m= 87 mr = 1336 m= 0 mr = 16 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 30252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22398 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) : 0.5692903 object centre at (A) : 27.94700 -12.45950 29.84150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1459516E-03 1.0388300E-02 midg,1,midg; midg,igrid,midg -3.5547055E-02 2.4847132E-03 1,midg,midg; igrid,midg,midg -2.8992429E-02 -5.7535372E-03 gauss-seidel spectral radius is 0.9983537 estimated iterations to convergence 196 setup time was (sec) 0.8600000 now iterating at: 07:02:15 rms-change max change #iterations 3.662070 166.8195 at 10iterations 1.585228 59.01845 at 20iterations 0.6888164 22.78692 at 30iterations 0.2989043 11.51305 at 40iterations 0.1303137 4.526532 at 50iterations 5.6595922E-02 1.854270 at 60iterations 2.4604786E-02 0.9164200 at 70iterations 1.0669677E-02 0.3533421 at 80iterations 4.6400139E-03 0.1502113 at 90iterations 2.0266157E-03 6.7733765E-02 at 100iterations 8.7975652E-04 3.4667969E-02 at 110iterations 3.8302303E-04 1.3626099E-02 at 120iterations finished qdiffx linear iterations at : 07:02:22 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 3.8302303E-04 1.3626099E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 07:02:22 8.087u 0.220s 0:08.75 94.8% 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 07:02:22 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 !!! WARNING: UMP 469 has a net charge of -0.1000 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: 2.561806 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): -3.320000 59.21400 ymin,ymax (A): -41.74600 16.82700 zmin,zma (A): 5.766000 53.91700 x,y,z range (A): 62.53400 58.57300 48.15100 scale (grids/A): 2.561806 object centre (A): 27.94700 -12.45950 29.84150 number of atom coordinates read : 3037 total number of charged atoms : 2893 net assigned charge : -4.099982 assigned positive charge : 444.8854 centred at (gu) : 97.22185 91.32076 92.01305 assigned negative charge : -448.9860 centred at (gu) : 96.53206 90.71025 92.18377 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 164929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26772 grid for indexing accessible points = 1.400000 m= 77490 mr = 118492 m= 23400 mr = 62290 m= 4045 mr = 18121 m= 377 mr = 2779 m= 7 mr = 215 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 68349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 23138 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) : 1.707871 object centre at (A) : 27.94700 -12.45950 29.84150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4387523E-02 0.1762637 midg,1,midg; midg,igrid,midg -0.6036595 0.1066738 1,midg,midg; igrid,midg,midg -0.5309035 -7.8675643E-02 gauss-seidel spectral radius is 0.9991918 estimated iterations to convergence 278 setup time was (sec) 1.600000 now iterating at: 07:02:24 rms-change max change #iterations 9.166573 343.2242 at 10iterations 5.223185 111.8337 at 20iterations 2.967150 63.33208 at 30iterations 1.675059 34.47079 at 40iterations 0.9461693 19.55994 at 50iterations 0.5313696 11.00218 at 60iterations 0.2991334 5.713638 at 70iterations 0.1679967 3.323007 at 80iterations 9.4330326E-02 1.779089 at 90iterations 5.2795038E-02 1.064088 at 100iterations 2.9587204E-02 0.6022339 at 110iterations 1.6620522E-02 0.3268299 at 120iterations 9.2744222E-03 0.1757317 at 130iterations 5.1991055E-03 9.5630646E-02 at 140iterations 2.9118494E-03 5.8080673E-02 at 150iterations 1.6310468E-03 3.2840729E-02 at 160iterations 9.1267627E-04 1.6539097E-02 at 170iterations 5.1071792E-04 9.7084045E-03 at 180iterations finished qdiffx linear iterations at : 07:02:35 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 5.1071792E-04 9.7084045E-03 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 07:02:36 13.042u 0.227s 0:13.73 96.5% 0+0k 0+0io 0pf+0w