Sat Oct 8 16:48:14 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 16:48:14 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4469 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5466159 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): 16.00000 79.22000 ymin,ymax (A): 118.7120 183.8400 zmin,zma (A): -1.078000 59.81000 x,y,z range (A): 63.22000 65.12800 60.88800 scale (grids/A): 0.5466159 object centre (A): 47.61000 151.2760 29.36600 number of atom coordinates read : 4469 total number of charged atoms : 4299 net assigned charge : 4.500035 assigned positive charge : 685.5988 centred at (gu) : 91.78510 89.70039 87.55588 assigned negative charge : -681.1019 centred at (gu) : 91.77325 89.63628 87.58822 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8475 nv = 96 ne = 84 npr = 90684 no. pairs analyzed = 90684 no. exposed pairs = 5449 no. arc points = 37126 no. surface atoms = 1826 nbur = 2643 mkacc time = 0.2400000 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 = 1.568000 m= 345 mr = 4545 m= 0 mr = 22 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3891 ## 522 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11390 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1166771E-09 -2.8311017E-11 midg,1,midg; midg,igrid,midg -4.2313045E-10 8.6357971E-10 1,midg,midg; igrid,midg,midg 1.0155879E-10 6.1491012E-10 gauss-seidel spectral radius is 0.9828508 estimated iterations to convergence 63 setup time was (sec) 0.7800000 now iterating at: 16:48:16 rms-change max change #iterations 9.3349233E-02 13.81648 at 10iterations 6.7795189E-03 0.9386826 at 20iterations 9.6629740E-04 0.1467247 at 30iterations 2.9611669E-04 4.4775009E-02 at 40iterations 1.0534542E-04 1.4699936E-02 at 50iterations finished qdiffx linear iterations at : 16:48:20 total time elapsed so far: 5.170000 # loops : 50 mean,max change (kT/e) : 1.0534542E-04 1.4699936E-02 energy calculations done at 5.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.340000 DelPhi exited at 16:48:20 5.344u 0.456s 0:06.09 95.0% 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 Sat Oct 8 2011 at 16:48:21 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4469 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: 1.639848 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): 16.00000 79.22000 ymin,ymax (A): 118.7120 183.8400 zmin,zma (A): -1.078000 59.81000 x,y,z range (A): 63.22000 65.12800 60.88800 scale (grids/A): 1.639848 object centre (A): 47.61000 151.2760 29.36600 number of atom coordinates read : 4469 total number of charged atoms : 4299 net assigned charge : 4.500035 assigned positive charge : 685.5988 centred at (gu) : 95.35446 89.09995 82.66661 assigned negative charge : -681.1019 centred at (gu) : 95.31952 88.90863 82.76434 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 95190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37126 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29766 mr = 66770 m= 3386 mr = 20216 m= 102 mr = 1787 m= 0 mr = 6 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 398 time to turn everything in is 0.8000000 number of dielectric boundary points 39665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 505 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 32966 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) : 0.5466159 object centre at (A) : 47.61000 151.2760 29.36600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4345050E-03 8.3269700E-03 midg,1,midg; midg,igrid,midg 1.2443439E-02 2.8403450E-02 1,midg,midg; igrid,midg,midg -1.1388752E-02 -1.4254656E-02 gauss-seidel spectral radius is 0.9983421 estimated iterations to convergence 195 setup time was (sec) 1.210000 now iterating at: 16:48:22 rms-change max change #iterations 4.253369 153.3408 at 10iterations 1.838697 59.01205 at 20iterations 0.7977490 27.71243 at 30iterations 0.3463770 10.37568 at 40iterations 0.1502609 5.139509 at 50iterations 6.5303579E-02 1.937180 at 60iterations 2.8386282E-02 0.9139562 at 70iterations 1.2396994E-02 0.3766556 at 80iterations 5.4553142E-03 0.1758118 at 90iterations 2.4318290E-03 8.5603237E-02 at 100iterations 1.1220330E-03 3.3355713E-02 at 110iterations 5.4547220E-04 1.6902924E-02 at 120iterations finished qdiffx linear iterations at : 16:48:34 total time elapsed so far: 12.65000 # loops : 120 mean,max change (kT/e) : 5.4547220E-04 1.6902924E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 16:48:34 12.829u 0.512s 0:13.66 97.5% 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 Sat Oct 8 2011 at 16:48:34 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4469 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: 2.459772 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): 16.00000 79.22000 ymin,ymax (A): 118.7120 183.8400 zmin,zma (A): -1.078000 59.81000 x,y,z range (A): 63.22000 65.12800 60.88800 scale (grids/A): 2.459772 object centre (A): 47.61000 151.2760 29.36600 number of atom coordinates read : 4469 total number of charged atoms : 4299 net assigned charge : 4.500035 assigned positive charge : 685.5988 centred at (gu) : 98.03136 88.64970 78.99948 assigned negative charge : -681.1019 centred at (gu) : 97.97906 88.36273 79.14641 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 221719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37126 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 103419 mr = 163585 m= 29851 mr = 81778 m= 5467 mr = 22155 m= 443 mr = 3857 m= 5 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 1400 time to turn everything in is 2.020000 number of dielectric boundary points 89328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 34337 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) : 1.639848 object centre at (A) : 47.61000 151.2760 29.36600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7261090E-04 0.1787688 midg,1,midg; midg,igrid,midg 0.2117134 0.4597958 1,midg,midg; igrid,midg,midg -0.1693313 -0.2549675 gauss-seidel spectral radius is 0.9992167 estimated iterations to convergence 282 setup time was (sec) 2.440000 now iterating at: 16:48:37 rms-change max change #iterations 11.06437 294.2460 at 10iterations 6.445936 128.6068 at 20iterations 3.720256 80.91695 at 30iterations 2.145081 39.66212 at 40iterations 1.229560 22.55285 at 50iterations 0.7024842 13.75043 at 60iterations 0.4005710 7.535348 at 70iterations 0.2278461 3.932864 at 80iterations 0.1296410 2.123077 at 90iterations 7.3597878E-02 1.277090 at 100iterations 4.1738853E-02 0.7279091 at 110iterations 2.3754604E-02 0.4237690 at 120iterations 1.3491866E-02 0.2492695 at 130iterations 7.6350248E-03 0.1441917 at 140iterations 4.3457313E-03 7.1392059E-02 at 150iterations 2.4715823E-03 4.1141510E-02 at 160iterations 1.4125005E-03 2.3477554E-02 at 170iterations 8.1217202E-04 1.3872147E-02 at 180iterations finished qdiffx linear iterations at : 16:48:57 total time elapsed so far: 22.14000 # loops : 180 mean,max change (kT/e) : 8.1217202E-04 1.3872147E-02 energy calculations done at 22.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.31000 DelPhi exited at 16:48:57 22.315u 0.536s 0:23.18 98.5% 0+0k 0+0io 0pf+0w