Sun Oct 9 16:53:25 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 16:53:25 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5215505 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): -23.02700 45.23100 ymin,ymax (A): -42.10700 22.46800 zmin,zma (A): 8.259001 70.46100 x,y,z range (A): 68.25800 64.57500 62.20200 scale (grids/A): 0.5215505 object centre (A): 11.10200 -9.819499 39.36000 number of atom coordinates read : 5350 total number of charged atoms : 5188 net assigned charge : 13.00004 assigned positive charge : 810.4926 centred at (gu) : 90.14119 89.75237 89.73945 assigned negative charge : -797.4986 centred at (gu) : 90.08191 89.57103 89.82713 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9366 nv = 96 ne = 84 npr = 104613 no. pairs analyzed = 104613 no. exposed pairs = 7092 no. arc points = 50188 no. surface atoms = 2331 nbur = 3019 mkacc time = 0.2700000 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 = 1.652000 m= 323 mr = 4716 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.5500000 number of dielectric boundary points 4968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4936 ## 775 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 12607 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4556328E-10 -9.9089903E-11 midg,1,midg; midg,igrid,midg -5.8999383E-10 1.0425973E-09 1,midg,midg; igrid,midg,midg 2.5288370E-11 5.9037547E-10 gauss-seidel spectral radius is 0.9812482 estimated iterations to convergence 60 setup time was (sec) 0.9000000 now iterating at: 16:53:26 rms-change max change #iterations 8.4310554E-02 12.54250 at 10iterations 8.4327320E-03 1.279575 at 20iterations 2.1771574E-03 0.2669067 at 30iterations 7.0771080E-04 8.2027435E-02 at 40iterations 2.4071000E-04 2.7004242E-02 at 50iterations finished qdiffx linear iterations at : 16:53:31 total time elapsed so far: 5.350000 # loops : 50 mean,max change (kT/e) : 2.4071000E-04 2.7004242E-02 energy calculations done at 5.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.530000 DelPhi exited at 16:53:31 5.533u 0.474s 0:06.27 95.6% 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 16:53:31 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.564652 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): -23.02700 45.23100 ymin,ymax (A): -42.10700 22.46800 zmin,zma (A): 8.259001 70.46100 x,y,z range (A): 68.25800 64.57500 62.20200 scale (grids/A): 1.564652 object centre (A): 11.10200 -9.819499 39.36000 number of atom coordinates read : 5350 total number of charged atoms : 5188 net assigned charge : 13.00004 assigned positive charge : 810.4926 centred at (gu) : 90.42219 89.25571 89.21633 assigned negative charge : -797.4986 centred at (gu) : 90.24536 88.71272 89.48087 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 105474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50188 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30649 mr = 70981 m= 2807 mr = 20039 m= 59 mr = 1229 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 324 time to turn everything in is 0.8800000 number of dielectric boundary points 46740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 705 ## 9 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 39259 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) : 0.5215505 object centre at (A) : 11.10200 -9.819499 39.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8048279E-02 1.5184048E-02 midg,1,midg; midg,igrid,midg -1.7750410E-02 3.5566811E-02 1,midg,midg; igrid,midg,midg -1.5285488E-02 2.3340639E-02 gauss-seidel spectral radius is 0.9982787 estimated iterations to convergence 191 setup time was (sec) 1.240000 now iterating at: 16:53:33 rms-change max change #iterations 4.291722 168.3928 at 10iterations 1.821112 64.54155 at 20iterations 0.7744771 22.38254 at 30iterations 0.3311277 10.61442 at 40iterations 0.1419518 4.063934 at 50iterations 6.0815379E-02 1.725967 at 60iterations 2.6233518E-02 0.7995605 at 70iterations 1.1544032E-02 0.3442935 at 80iterations 5.2232072E-03 0.1602802 at 90iterations 2.5029760E-03 8.1504822E-02 at 100iterations 1.2993596E-03 3.7057877E-02 at 110iterations 7.3933677E-04 1.9599915E-02 at 120iterations finished qdiffx linear iterations at : 16:53:45 total time elapsed so far: 12.94000 # loops : 120 mean,max change (kT/e) : 7.3933677E-04 1.9599915E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 16:53:45 13.106u 0.536s 0:13.98 97.4% 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 Sun Oct 9 2011 at 16:53:45 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.346977 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): -23.02700 45.23100 ymin,ymax (A): -42.10700 22.46800 zmin,zma (A): 8.259001 70.46100 x,y,z range (A): 68.25800 64.57500 62.20200 scale (grids/A): 2.346977 object centre (A): 11.10200 -9.819499 39.36000 number of atom coordinates read : 5350 total number of charged atoms : 5188 net assigned charge : 13.00004 assigned positive charge : 810.4926 centred at (gu) : 90.63252 88.88301 88.82413 assigned negative charge : -797.4986 centred at (gu) : 90.36785 88.06889 89.22131 start vw surface at 0.1800000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 245439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50188 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 108965 mr = 174870 m= 27868 mr = 83608 m= 4091 mr = 19959 m= 221 mr = 2526 m= 4 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 1156 time to turn everything in is 2.210000 number of dielectric boundary points 105562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 2.400000 number of grid points assigned charge 41426 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) : 1.564652 object centre at (A) : 11.10200 -9.819499 39.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6496816 0.2711921 midg,1,midg; midg,igrid,midg -0.3236771 0.5646830 1,midg,midg; igrid,midg,midg -0.4458971 0.3602945 gauss-seidel spectral radius is 0.9992338 estimated iterations to convergence 285 setup time was (sec) 2.630000 now iterating at: 16:53:48 rms-change max change #iterations 11.47198 307.7316 at 10iterations 6.808809 171.4073 at 20iterations 4.010835 89.21503 at 30iterations 2.343356 49.24260 at 40iterations 1.358953 28.95365 at 50iterations 0.7876906 15.85718 at 60iterations 0.4552131 9.247019 at 70iterations 0.2617607 4.900434 at 80iterations 0.1507348 3.107393 at 90iterations 8.6521767E-02 1.557043 at 100iterations 4.9645722E-02 0.9084356 at 110iterations 2.8455900E-02 0.4990654 at 120iterations 1.6359396E-02 0.2953739 at 130iterations 9.3902824E-03 0.1721249 at 140iterations 5.3982725E-03 9.2109680E-02 at 150iterations 3.1156051E-03 6.3175201E-02 at 160iterations 1.8185443E-03 2.8950691E-02 at 170iterations 1.0777354E-03 1.9561768E-02 at 180iterations finished qdiffx linear iterations at : 16:54:09 total time elapsed so far: 23.34000 # loops : 180 mean,max change (kT/e) : 1.0777354E-03 1.9561768E-02 energy calculations done at 23.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.50000 DelPhi exited at 16:54:10 23.508u 0.552s 0:24.36 98.7% 0+0k 0+0io 0pf+0w