Sat Oct 8 17:07:49 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 Sat Oct 8 2011 at 17:07:49 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5173817 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): -14.66900 44.43500 ymin,ymax (A): -39.35400 29.45400 zmin,zma (A): -16.62700 35.08300 x,y,z range (A): 59.10400 68.80800 51.71000 scale (grids/A): 0.5173817 object centre (A): 14.88300 -4.950000 9.228000 number of atom coordinates read : 3516 total number of charged atoms : 3370 net assigned charge : -3.999990 assigned positive charge : 534.1112 centred at (gu) : 90.59528 91.94820 90.55176 assigned negative charge : -538.1129 centred at (gu) : 90.61017 91.94238 90.50895 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5928 nv = 96 ne = 84 npr = 71724 no. pairs analyzed = 71724 no. exposed pairs = 4327 no. arc points = 29884 no. surface atoms = 1458 nbur = 2058 mkacc time = 0.2300000 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 = 1.680000 m= 213 mr = 3129 m= 0 mr = 5 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 3007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3029 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 8024 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6324309E-10 3.9103779E-11 midg,1,midg; midg,igrid,midg -5.6293432E-11 -1.0122259E-10 1,midg,midg; igrid,midg,midg -3.3309473E-11 -1.3462860E-10 gauss-seidel spectral radius is 0.9807987 estimated iterations to convergence 60 setup time was (sec) 0.7600000 now iterating at: 17:07:50 rms-change max change #iterations 6.1402753E-02 9.438816 at 10iterations 3.7093770E-03 0.7059660 at 20iterations 4.4365882E-04 7.6451302E-02 at 30iterations 1.1140046E-04 2.1155357E-02 at 40iterations 3.1881202E-05 6.0701370E-03 at 50iterations finished qdiffx linear iterations at : 17:07:54 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 3.1881202E-05 6.0701370E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 17:07:54 4.657u 0.432s 0:05.38 94.4% 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 Sat Oct 8 2011 at 17:07:54 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.552145 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): -14.66900 44.43500 ymin,ymax (A): -39.35400 29.45400 zmin,zma (A): -16.62700 35.08300 x,y,z range (A): 59.10400 68.80800 51.71000 scale (grids/A): 1.552145 object centre (A): 14.88300 -4.950000 9.228000 number of atom coordinates read : 3516 total number of charged atoms : 3370 net assigned charge : -3.999990 assigned positive charge : 534.1112 centred at (gu) : 91.78444 95.84382 91.65424 assigned negative charge : -538.1129 centred at (gu) : 91.83012 95.82663 91.52611 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 67092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29884 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19881 mr = 46320 m= 1845 mr = 13543 m= 41 mr = 854 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 167 time to turn everything in is 0.7000000 number of dielectric boundary points 28142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 410 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 25460 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) : 0.5173817 object centre at (A) : 14.88300 -4.950000 9.228000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1993621E-03 2.4046521E-03 midg,1,midg; midg,igrid,midg 1.0111587E-02 2.1853566E-03 1,midg,midg; igrid,midg,midg -4.3690344E-03 -1.1572252E-02 gauss-seidel spectral radius is 0.9980283 estimated iterations to convergence 179 setup time was (sec) 1.080000 now iterating at: 17:07:56 rms-change max change #iterations 3.299773 159.9576 at 10iterations 1.325639 52.69608 at 20iterations 0.5323551 19.97188 at 30iterations 0.2151104 7.770407 at 40iterations 8.6330831E-02 3.097874 at 50iterations 3.4830078E-02 1.249502 at 60iterations 1.4081403E-02 0.5381713 at 70iterations 5.6911004E-03 0.2224312 at 80iterations 2.3140919E-03 9.0438843E-02 at 90iterations 9.5146889E-04 3.3163071E-02 at 100iterations 4.0686017E-04 1.4874935E-02 at 110iterations 1.8509576E-04 8.2225800E-03 at 120iterations finished qdiffx linear iterations at : 17:08:05 total time elapsed so far: 10.07000 # loops : 120 mean,max change (kT/e) : 1.8509576E-04 8.2225800E-03 energy calculations done at 10.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 17:08:05 10.283u 0.454s 0:11.07 96.9% 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 Sat Oct 8 2011 at 17:08:05 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.328218 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): -14.66900 44.43500 ymin,ymax (A): -39.35400 29.45400 zmin,zma (A): -16.62700 35.08300 x,y,z range (A): 59.10400 68.80800 51.71000 scale (grids/A): 2.328218 object centre (A): 14.88300 -4.950000 9.228000 number of atom coordinates read : 3516 total number of charged atoms : 3370 net assigned charge : -3.999990 assigned positive charge : 534.1112 centred at (gu) : 92.67657 98.76568 92.48124 assigned negative charge : -538.1129 centred at (gu) : 92.74491 98.73991 92.28914 start vw surface at 0.1800000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 156214 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29884 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70782 mr = 113324 m= 18485 mr = 56129 m= 2602 mr = 13545 m= 159 mr = 1633 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 612 time to turn everything in is 1.710000 number of dielectric boundary points 63559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 26890 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) : 1.552145 object centre at (A) : 14.88300 -4.950000 9.228000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9629754E-02 4.4837184E-02 midg,1,midg; midg,igrid,midg 0.3401444 9.8233549E-03 1,midg,midg; igrid,midg,midg -6.2515482E-02 -0.1569871 gauss-seidel spectral radius is 0.9990948 estimated iterations to convergence 263 setup time was (sec) 2.070000 now iterating at: 17:08:08 rms-change max change #iterations 8.741339 254.9920 at 10iterations 4.807493 120.3404 at 20iterations 2.631281 58.01106 at 30iterations 1.438165 34.77804 at 40iterations 0.7831996 17.33016 at 50iterations 0.4260899 8.746778 at 60iterations 0.2312558 5.304825 at 70iterations 0.1255236 2.826256 at 80iterations 6.8060838E-02 1.577778 at 90iterations 3.6812026E-02 0.7896008 at 100iterations 1.9952839E-02 0.5087299 at 110iterations 1.0868301E-02 0.2262630 at 120iterations 5.8988207E-03 0.1282363 at 130iterations 3.2209416E-03 6.8305969E-02 at 140iterations 1.7604718E-03 3.5644531E-02 at 150iterations 9.7597000E-04 2.2737503E-02 at 160iterations 5.5154599E-04 1.3727546E-02 at 170iterations 3.2175882E-04 7.6255798E-03 at 180iterations finished qdiffx linear iterations at : 17:08:24 total time elapsed so far: 17.85000 # loops : 180 mean,max change (kT/e) : 3.2175882E-04 7.6255798E-03 energy calculations done at 17.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.08000 DelPhi exited at 17:08:24 18.084u 0.482s 0:18.85 98.4% 0+0k 0+0io 0pf+0w