Sun Oct 16 14:13:07 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 Sun Oct 16 2011 at 14:13:07 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 = 2287 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: 0.6427037 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): -2.065000 46.48000 ymin,ymax (A): -15.27500 30.06600 zmin,zma (A): -19.13400 36.25700 x,y,z range (A): 48.54500 45.34100 55.39100 scale (grids/A): 0.6427037 object centre (A): 22.20750 7.395500 8.561501 number of atom coordinates read : 2287 total number of charged atoms : 2223 net assigned charge : 5.000002 assigned positive charge : 340.7432 centred at (gu) : 90.27481 88.40987 90.12209 assigned negative charge : -335.7438 centred at (gu) : 90.33411 88.54359 90.12285 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6383 nv = 96 ne = 84 npr = 45909 no. pairs analyzed = 45909 no. exposed pairs = 2879 no. arc points = 20067 no. surface atoms = 987 nbur = 1300 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3496 m= 0 mr = 40 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2700000 number of dielectric boundary points 3191 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1974 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7768 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5091222E-09 7.7271869E-09 midg,1,midg; midg,igrid,midg 3.0842266E-08 -4.9254534E-09 1,midg,midg; igrid,midg,midg 1.3215819E-08 1.1936083E-09 gauss-seidel spectral radius is 0.9874305 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 14:13:08 rms-change max change #iterations 0.1343061 19.82789 at 10iterations 1.3412936E-02 2.123451 at 20iterations 1.3815822E-03 0.2399216 at 30iterations 1.6948429E-04 2.7456999E-02 at 40iterations 3.3606539E-05 5.9475452E-03 at 50iterations finished qdiffx linear iterations at : 14:13:15 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 3.3606539E-05 5.9475452E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 14:13:16 3.555u 0.163s 0:09.63 38.5% 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 16 2011 at 14:13:17 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 = 2287 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.928111 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): -2.065000 46.48000 ymin,ymax (A): -15.27500 30.06600 zmin,zma (A): -19.13400 36.25700 x,y,z range (A): 48.54500 45.34100 55.39100 scale (grids/A): 1.928111 object centre (A): 22.20750 7.395500 8.561501 number of atom coordinates read : 2287 total number of charged atoms : 2223 net assigned charge : 5.000002 assigned positive charge : 340.7432 centred at (gu) : 90.82406 85.22919 90.36569 assigned negative charge : -335.7438 centred at (gu) : 91.00230 85.63078 90.36838 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20067 grid for indexing accessible points = 1.400000 m= 24955 mr = 47743 m= 4197 mr = 18358 m= 240 mr = 2709 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1507 time to turn everything in is 0.5300000 number of dielectric boundary points 29428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17465 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) : 0.6427037 object centre at (A) : 22.20750 7.395500 8.561501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3841646E-02 1.3018477E-02 midg,1,midg; midg,igrid,midg 2.7234126E-02 -2.8896627E-03 1,midg,midg; igrid,midg,midg 5.3856336E-03 -3.5017133E-02 gauss-seidel spectral radius is 0.9986358 estimated iterations to convergence 215 setup time was (sec) 0.8300000 now iterating at: 14:13:18 rms-change max change #iterations 4.033659 195.3309 at 10iterations 1.881843 75.54934 at 20iterations 0.8838851 30.83724 at 30iterations 0.4164800 15.23092 at 40iterations 0.1949657 6.810205 at 50iterations 9.1371708E-02 3.084832 at 60iterations 4.2757075E-02 1.358413 at 70iterations 2.0109946E-02 0.6133919 at 80iterations 9.4612595E-03 0.3487301 at 90iterations 4.4208877E-03 0.1327219 at 100iterations 2.0819572E-03 7.1162701E-02 at 110iterations 9.7727112E-04 3.1724930E-02 at 120iterations finished qdiffx linear iterations at : 14:13:24 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 9.7727112E-04 3.1724930E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 14:13:25 7.620u 0.193s 0:08.08 96.6% 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 16 2011 at 14:13:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2287 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.892167 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): -2.065000 46.48000 ymin,ymax (A): -15.27500 30.06600 zmin,zma (A): -19.13400 36.25700 x,y,z range (A): 48.54500 45.34100 55.39100 scale (grids/A): 2.892167 object centre (A): 22.20750 7.395500 8.561501 number of atom coordinates read : 2287 total number of charged atoms : 2223 net assigned charge : 5.000002 assigned positive charge : 340.7432 centred at (gu) : 91.23601 82.84370 90.54835 assigned negative charge : -335.7438 centred at (gu) : 91.50341 83.44629 90.55251 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 159734 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20067 grid for indexing accessible points = 1.400000 m= 80194 mr = 116294 m= 29946 mr = 65193 m= 7577 mr = 24066 m= 1083 mr = 5857 m= 72 mr = 684 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 5117 time to turn everything in is 1.340000 number of dielectric boundary points 66473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 17783 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) : 1.928111 object centre at (A) : 22.20750 7.395500 8.561501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2310486 8.8189095E-02 midg,1,midg; midg,igrid,midg 0.2232245 -4.1919157E-02 1,midg,midg; igrid,midg,midg 5.3826019E-02 -0.4819702 gauss-seidel spectral radius is 0.9992572 estimated iterations to convergence 290 setup time was (sec) 1.670000 now iterating at: 14:13:27 rms-change max change #iterations 9.407810 396.6618 at 10iterations 5.516067 123.9426 at 20iterations 3.207495 73.65273 at 30iterations 1.868758 39.39146 at 40iterations 1.083931 21.12993 at 50iterations 0.6274231 13.64520 at 60iterations 0.3633215 7.431149 at 70iterations 0.2090649 3.731350 at 80iterations 0.1206488 2.291674 at 90iterations 6.9712475E-02 1.272352 at 100iterations 4.0093668E-02 0.7826633 at 110iterations 2.3079099E-02 0.4914856 at 120iterations 1.3256977E-02 0.2321997 at 130iterations 7.6252036E-03 0.1500177 at 140iterations 4.3835263E-03 8.3320618E-02 at 150iterations 2.5170937E-03 5.5018425E-02 at 160iterations 1.4482802E-03 3.0200958E-02 at 170iterations 8.3279266E-04 1.6759157E-02 at 180iterations finished qdiffx linear iterations at : 14:13:38 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 8.3279266E-04 1.6759157E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 14:13:38 12.869u 0.179s 0:13.36 97.5% 0+0k 0+0io 0pf+0w