Sat Oct 15 14:58:57 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+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 15 2011 at 14:58:57 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! WARNING: HIR 121 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6013920 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): -10.21000 40.64300 ymin,ymax (A): 30.49200 89.68800 zmin,zma (A): -10.13700 45.67600 x,y,z range (A): 50.85300 59.19600 55.81300 scale (grids/A): 0.6013920 object centre (A): 15.21650 60.09000 17.76950 number of atom coordinates read : 2710 total number of charged atoms : 2572 net assigned charge : 0.5140082 assigned positive charge : 401.1717 centred at (gu) : 90.57490 89.34432 89.45140 assigned negative charge : -400.6588 centred at (gu) : 90.57898 89.37071 89.47379 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6614 nv = 96 ne = 84 npr = 54260 no. pairs analyzed = 54260 no. exposed pairs = 3894 no. arc points = 27701 no. surface atoms = 1281 nbur = 1429 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3136 m= 0 mr = 14 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2738 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2426475E-09 -5.8441491E-10 midg,1,midg; midg,igrid,midg 1.4556502E-09 -7.0596445E-10 1,midg,midg; igrid,midg,midg 3.3288258E-10 6.3834278E-11 gauss-seidel spectral radius is 0.9857118 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 14:58:58 rms-change max change #iterations 0.1058598 19.65029 at 10iterations 9.1757486E-03 1.373335 at 20iterations 8.2541135E-04 0.1407051 at 30iterations 7.9840669E-05 1.2237549E-02 at 40iterations 1.0087487E-05 1.4972687E-03 at 50iterations finished qdiffx linear iterations at : 14:59:01 total time elapsed so far: 3.710000 # loops : 50 mean,max change (kT/e) : 1.0087487E-05 1.4972687E-03 energy calculations done at 3.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 14:59:01 3.876u 0.238s 0:04.43 92.5% 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 15 2011 at 14:59:01 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! WARNING: HIR 121 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.804176 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): -10.21000 40.64300 ymin,ymax (A): 30.49200 89.68800 zmin,zma (A): -10.13700 45.67600 x,y,z range (A): 50.85300 59.19600 55.81300 scale (grids/A): 1.804176 object centre (A): 15.21650 60.09000 17.76950 number of atom coordinates read : 2710 total number of charged atoms : 2572 net assigned charge : 0.5140082 assigned positive charge : 401.1717 centred at (gu) : 91.72411 88.03218 88.35340 assigned negative charge : -400.6588 centred at (gu) : 91.73689 88.11192 88.42130 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27701 grid for indexing accessible points = 1.400000 m= 23354 mr = 45174 m= 3264 mr = 15553 m= 148 mr = 1609 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 34941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20073 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) : 0.6013920 object centre at (A) : 15.21650 60.09000 17.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9477028E-03 -1.9735646E-02 midg,1,midg; midg,igrid,midg 2.3898026E-02 -1.8452916E-02 1,midg,midg; igrid,midg,midg 2.1788706E-03 -5.3825747E-04 gauss-seidel spectral radius is 0.9985158 estimated iterations to convergence 206 setup time was (sec) 0.6300000 now iterating at: 14:59:02 rms-change max change #iterations 3.879229 186.5537 at 10iterations 1.735335 65.09062 at 20iterations 0.7858008 30.69735 at 30iterations 0.3550380 11.60221 at 40iterations 0.1601019 5.441528 at 50iterations 7.2245583E-02 2.387394 at 60iterations 3.2845084E-02 1.220717 at 70iterations 1.4804299E-02 0.4933262 at 80iterations 6.7299078E-03 0.2247257 at 90iterations 3.0373582E-03 0.1044655 at 100iterations 1.3715978E-03 5.1772118E-02 at 110iterations 6.2350178E-04 1.9234657E-02 at 120iterations finished qdiffx linear iterations at : 14:59:10 total time elapsed so far: 8.760000 # loops : 120 mean,max change (kT/e) : 6.2350178E-04 1.9234657E-02 energy calculations done at 8.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.890000 DelPhi exited at 14:59:11 8.896u 0.265s 0:09.43 97.0% 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 15 2011 at 14:59:11 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! WARNING: HIR 121 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.706264 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): -10.21000 40.64300 ymin,ymax (A): 30.49200 89.68800 zmin,zma (A): -10.13700 45.67600 x,y,z range (A): 50.85300 59.19600 55.81300 scale (grids/A): 2.706264 object centre (A): 15.21650 60.09000 17.76950 number of atom coordinates read : 2710 total number of charged atoms : 2572 net assigned charge : 0.5140082 assigned positive charge : 401.1717 centred at (gu) : 92.58596 87.04821 87.52998 assigned negative charge : -400.6588 centred at (gu) : 92.60537 87.16788 87.63183 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 163598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27701 grid for indexing accessible points = 1.400000 m= 76060 mr = 111502 m= 25950 mr = 58507 m= 5466 mr = 19052 m= 589 mr = 3440 m= 15 mr = 282 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 78893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 20563 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) : 1.804176 object centre at (A) : 15.21650 60.09000 17.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9717248E-02 -0.2724508 midg,1,midg; midg,igrid,midg 0.4125653 -0.1731460 1,midg,midg; igrid,midg,midg 7.3294327E-02 -2.6899481E-02 gauss-seidel spectral radius is 0.9992407 estimated iterations to convergence 286 setup time was (sec) 1.240000 now iterating at: 14:59:12 rms-change max change #iterations 9.633512 348.8300 at 10iterations 5.710920 178.5467 at 20iterations 3.340786 84.14733 at 30iterations 1.941615 49.14812 at 40iterations 1.125387 22.38874 at 50iterations 0.6489378 13.82890 at 60iterations 0.3740025 7.400410 at 70iterations 0.2150232 4.642185 at 80iterations 0.1229824 2.406112 at 90iterations 7.0360266E-02 1.405600 at 100iterations 4.0178869E-02 0.7753906 at 110iterations 2.3024561E-02 0.4963684 at 120iterations 1.3140531E-02 0.2500648 at 130iterations 7.4927937E-03 0.1510258 at 140iterations 4.2874985E-03 7.9419136E-02 at 150iterations 2.4506517E-03 4.4765472E-02 at 160iterations 1.4015008E-03 2.5138855E-02 at 170iterations 8.0266321E-04 1.5482157E-02 at 180iterations finished qdiffx linear iterations at : 14:59:26 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 8.0266321E-04 1.5482157E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 14:59:26 13.476u 0.282s 0:15.55 88.4% 0+0k 0+0io 0pf+0w