Sun Oct 9 14:40:40 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 Sun Oct 9 2011 at 14:40:40 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1383 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: 0.8989899 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): -2.084000 37.51600 ymin,ymax (A): -14.32200 21.17400 zmin,zma (A): -14.78600 23.35900 x,y,z range (A): 39.60000 35.49600 38.14500 scale (grids/A): 0.8989899 object centre (A): 17.71600 3.426000 4.286501 number of atom coordinates read : 1383 total number of charged atoms : 1252 net assigned charge : 0.5000027 assigned positive charge : 205.5293 centred at (gu) : 89.95010 90.52755 90.85246 assigned negative charge : -205.0291 centred at (gu) : 89.65374 90.45825 91.06985 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7747 nv = 96 ne = 84 npr = 30029 no. pairs analyzed = 30029 no. exposed pairs = 1675 no. arc points = 12261 no. surface atoms = 566 nbur = 817 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 799 mr = 4495 m= 12 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 677 ## 59 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6683 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9069389E-06 -2.1900089E-06 midg,1,midg; midg,igrid,midg -4.3791215E-07 8.9847231E-07 1,midg,midg; igrid,midg,midg -2.6996775E-06 2.8753502E-06 gauss-seidel spectral radius is 0.9934598 estimated iterations to convergence 100 setup time was (sec) 0.4800000 now iterating at: 14:40:41 rms-change max change #iterations 0.4066885 51.45672 at 10iterations 7.7821054E-02 10.29919 at 20iterations 1.5029198E-02 2.443310 at 30iterations 2.8404626E-03 0.3412228 at 40iterations 5.3979823E-04 6.3430786E-02 at 50iterations finished qdiffx linear iterations at : 14:40:43 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 5.3979823E-04 6.3430786E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:40:44 3.325u 0.143s 0:03.82 90.5% 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 Sun Oct 9 2011 at 14:40:44 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1383 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: 2.696970 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): -2.084000 37.51600 ymin,ymax (A): -14.32200 21.17400 zmin,zma (A): -14.78600 23.35900 x,y,z range (A): 39.60000 35.49600 38.14500 scale (grids/A): 2.696970 object centre (A): 17.71600 3.426000 4.286501 number of atom coordinates read : 1383 total number of charged atoms : 1252 net assigned charge : 0.5000027 assigned positive charge : 205.5293 centred at (gu) : 89.85049 91.58279 92.55769 assigned negative charge : -205.0291 centred at (gu) : 88.96136 91.37470 93.20961 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 79264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12261 grid for indexing accessible points = 1.400000 m= 36576 mr = 55120 m= 11136 mr = 29285 m= 2122 mr = 8404 m= 192 mr = 1355 m= 5 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 35036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 10014 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) : 0.8989899 object centre at (A) : 17.71600 3.426000 4.286501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8060677E-02 1.0728138E-02 midg,1,midg; midg,igrid,midg -6.2494591E-02 -7.8508526E-02 1,midg,midg; igrid,midg,midg 2.1265691E-02 0.1153399 gauss-seidel spectral radius is 0.9991348 estimated iterations to convergence 269 setup time was (sec) 0.9500000 now iterating at: 14:40:45 rms-change max change #iterations 5.483118 288.1426 at 10iterations 3.020276 85.03510 at 20iterations 1.655633 48.74132 at 30iterations 0.9034390 24.65345 at 40iterations 0.4950875 12.95295 at 50iterations 0.2709825 7.619171 at 60iterations 0.1484672 4.113953 at 70iterations 8.1502073E-02 2.184826 at 80iterations 4.4532705E-02 1.104828 at 90iterations 2.4382859E-02 0.7024689 at 100iterations 1.3373611E-02 0.3645782 at 110iterations 7.3522325E-03 0.1929398 at 120iterations finished qdiffx linear iterations at : 14:40:52 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 7.3522325E-03 0.1929398 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 14:40:52 7.925u 0.172s 0:08.38 96.5% 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 Sun Oct 9 2011 at 14:40:52 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1383 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: 4.045455 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): -2.084000 37.51600 ymin,ymax (A): -14.32200 21.17400 zmin,zma (A): -14.78600 23.35900 x,y,z range (A): 39.60000 35.49600 38.14500 scale (grids/A): 4.045455 object centre (A): 17.71600 3.426000 4.286501 number of atom coordinates read : 1383 total number of charged atoms : 1252 net assigned charge : 0.5000027 assigned positive charge : 205.5293 centred at (gu) : 89.77580 92.37431 93.83652 assigned negative charge : -205.0291 centred at (gu) : 88.44202 92.06209 94.81441 start vw surface at 0.1300000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 181673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12261 grid for indexing accessible points = 1.400000 m= 104773 mr = 131964 m= 54931 mr = 89095 m= 22491 mr = 47446 m= 7401 mr = 18573 m= 1963 mr = 5849 m= 301 mr = 1506 m= 15 mr = 192 m= 0 mr = 1 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.210000 number of dielectric boundary points 78922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.340000 number of grid points assigned charge 10016 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) : 2.696970 object centre at (A) : 17.71600 3.426000 4.286501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5144781 0.1691350 midg,1,midg; midg,igrid,midg -0.3650878 -0.6230340 1,midg,midg; igrid,midg,midg 0.6072192 0.4758317 gauss-seidel spectral radius is 0.9993455 estimated iterations to convergence 308 setup time was (sec) 2.510000 now iterating at: 14:40:55 rms-change max change #iterations 10.99885 230.3009 at 10iterations 6.523362 124.2662 at 20iterations 3.872566 66.90347 at 30iterations 2.304105 37.42525 at 40iterations 1.368806 21.14682 at 50iterations 0.8155885 12.08378 at 60iterations 0.4823775 7.302510 at 70iterations 0.2875957 4.272326 at 80iterations 0.1705310 2.635128 at 90iterations 0.1015122 1.503482 at 100iterations 6.0498871E-02 0.9400826 at 110iterations 3.6263324E-02 0.5531082 at 120iterations 2.1833343E-02 0.3295727 at 130iterations 1.3350351E-02 0.2200050 at 140iterations 8.3634965E-03 0.1575279 at 150iterations 5.4759188E-03 0.1123810 at 160iterations 3.8020825E-03 7.7373505E-02 at 170iterations 2.8160543E-03 5.8551788E-02 at 180iterations finished qdiffx linear iterations at : 14:41:05 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 2.8160543E-03 5.8551788E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 14:41:06 13.209u 0.188s 0:13.67 97.8% 0+0k 0+0io 0pf+0w