Sat Oct 8 15:47:57 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+sph.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 = amb.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 15:47:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 0.6479443 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): -2.211000 46.02900 ymin,ymax (A): -16.97100 29.56600 zmin,zma (A): -18.64100 36.30200 x,y,z range (A): 48.24000 46.53700 54.94300 scale (grids/A): 0.6479443 object centre (A): 21.90900 6.297500 8.830500 number of atom coordinates read : 2358 total number of charged atoms : 2299 net assigned charge : 3.000007 assigned positive charge : 352.3040 centred at (gu) : 90.82493 88.95557 90.23289 assigned negative charge : -349.3047 centred at (gu) : 90.89126 89.06889 90.28023 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 46825 no. pairs analyzed = 46825 no. exposed pairs = 2999 no. arc points = 20652 no. surface atoms = 1024 nbur = 1334 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 363 mr = 3765 m= 0 mr = 49 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2032 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8136 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0964584E-08 -8.3446838E-10 midg,1,midg; midg,igrid,midg 2.4924869E-08 -7.5330702E-09 1,midg,midg; igrid,midg,midg 1.1729327E-08 -3.9815986E-09 gauss-seidel spectral radius is 0.9876389 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 15:47:58 rms-change max change #iterations 0.1453445 30.48038 at 10iterations 1.4808835E-02 2.001539 at 20iterations 1.5417631E-03 0.2102394 at 30iterations 1.8829927E-04 2.6832581E-02 at 40iterations 3.3218428E-05 4.7035217E-03 at 50iterations finished qdiffx linear iterations at : 15:48:02 total time elapsed so far: 5.070000 # loops : 50 mean,max change (kT/e) : 3.3218428E-05 4.7035217E-03 energy calculations done at 5.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 15:48:03 5.245u 0.439s 0:05.94 95.4% 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 15:48:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 1.943833 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): -2.211000 46.02900 ymin,ymax (A): -16.97100 29.56600 zmin,zma (A): -18.64100 36.30200 x,y,z range (A): 48.24000 46.53700 54.94300 scale (grids/A): 1.943833 object centre (A): 21.90900 6.297500 8.830500 number of atom coordinates read : 2358 total number of charged atoms : 2299 net assigned charge : 3.000007 assigned positive charge : 352.3040 centred at (gu) : 92.47435 86.86640 90.69811 assigned negative charge : -349.3047 centred at (gu) : 92.67368 87.20676 90.84054 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20652 grid for indexing accessible points = 1.400000 m= 26598 mr = 51196 m= 4448 mr = 19632 m= 257 mr = 2910 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 797 time to turn everything in is 0.6200000 number of dielectric boundary points 30692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 18155 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) : 0.6479443 object centre at (A) : 21.90900 6.297500 8.830500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8529542E-02 8.0600474E-03 midg,1,midg; midg,igrid,midg 1.9944672E-02 -5.6297630E-03 1,midg,midg; igrid,midg,midg 6.7900247E-03 -4.6176713E-02 gauss-seidel spectral radius is 0.9986680 estimated iterations to convergence 217 setup time was (sec) 0.9600000 now iterating at: 15:48:04 rms-change max change #iterations 4.171839 180.9927 at 10iterations 1.966301 100.9613 at 20iterations 0.9303490 31.84273 at 30iterations 0.4411420 16.27376 at 40iterations 0.2088980 6.712799 at 50iterations 9.8990001E-02 3.156643 at 60iterations 4.6831839E-02 1.383402 at 70iterations 2.2210399E-02 0.7316811 at 80iterations 1.0539321E-02 0.3432531 at 90iterations 4.9943607E-03 0.1670361 at 100iterations 2.3722558E-03 7.5071096E-02 at 110iterations 1.1311901E-03 3.5096169E-02 at 120iterations finished qdiffx linear iterations at : 15:48:16 total time elapsed so far: 12.91000 # loops : 120 mean,max change (kT/e) : 1.1311901E-03 3.5096169E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 15:48:17 13.086u 0.526s 0:13.88 97.9% 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 15:48:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.915749 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): -2.211000 46.02900 ymin,ymax (A): -16.97100 29.56600 zmin,zma (A): -18.64100 36.30200 x,y,z range (A): 48.24000 46.53700 54.94300 scale (grids/A): 2.915749 object centre (A): 21.90900 6.297500 8.830500 number of atom coordinates read : 2358 total number of charged atoms : 2299 net assigned charge : 3.000007 assigned positive charge : 352.3040 centred at (gu) : 93.71143 85.29943 91.04700 assigned negative charge : -349.3047 centred at (gu) : 94.01046 85.81008 91.26073 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 169409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20652 grid for indexing accessible points = 1.400000 m= 85446 mr = 124042 m= 31910 mr = 70056 m= 8317 mr = 25902 m= 1147 mr = 6326 m= 48 mr = 738 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 2580 time to turn everything in is 1.690000 number of dielectric boundary points 69207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 18388 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) : 1.943833 object centre at (A) : 21.90900 6.297500 8.830500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3298620 7.7623472E-02 midg,1,midg; midg,igrid,midg 0.1273280 -9.7164124E-02 1,midg,midg; igrid,midg,midg 7.8680016E-02 -0.5947720 gauss-seidel spectral radius is 0.9992681 estimated iterations to convergence 292 setup time was (sec) 2.090000 now iterating at: 15:48:19 rms-change max change #iterations 9.761244 509.7643 at 10iterations 5.740106 145.3435 at 20iterations 3.358646 76.26334 at 30iterations 1.965553 47.77560 at 40iterations 1.145729 22.37038 at 50iterations 0.6666397 12.99875 at 60iterations 0.3864236 7.509879 at 70iterations 0.2239211 4.193701 at 80iterations 0.1300753 2.340927 at 90iterations 7.5236827E-02 1.419297 at 100iterations 4.3400273E-02 0.8455861 at 110iterations 2.5123898E-02 0.4570255 at 120iterations 1.4524062E-02 0.2811813 at 130iterations 8.3737839E-03 0.1520844 at 140iterations 4.8355684E-03 8.1655502E-02 at 150iterations 2.7879223E-03 5.0935745E-02 at 160iterations 1.6126739E-03 2.8419971E-02 at 170iterations 9.3328138E-04 1.6572952E-02 at 180iterations finished qdiffx linear iterations at : 15:48:40 total time elapsed so far: 22.98000 # loops : 180 mean,max change (kT/e) : 9.3328138E-04 1.6572952E-02 energy calculations done at 22.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.14000 DelPhi exited at 15:48:41 23.146u 0.539s 0:23.93 98.9% 0+0k 0+0io 0pf+0w