Sat Oct 8 17:39:28 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 17:39:28 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 = 3741 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5391979 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): -28.38700 33.46200 ymin,ymax (A): -34.11100 31.91300 zmin,zma (A): 9.104000 63.37600 x,y,z range (A): 61.84900 66.02400 54.27200 scale (grids/A): 0.5391979 object centre (A): 2.537499 -1.099000 36.24000 number of atom coordinates read : 3741 total number of charged atoms : 3592 net assigned charge : -8.999979 assigned positive charge : 567.7997 centred at (gu) : 89.03574 90.32905 90.73141 assigned negative charge : -576.8017 centred at (gu) : 89.09080 90.34484 90.73935 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6831 nv = 96 ne = 84 npr = 76708 no. pairs analyzed = 76708 no. exposed pairs = 4560 no. arc points = 31288 no. surface atoms = 1543 nbur = 2198 mkacc time = 0.2000000 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 = 1.596000 m= 263 mr = 3648 m= 0 mr = 8 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3174 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9140 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1707678E-10 -5.7898636E-10 midg,1,midg; midg,igrid,midg -3.0125308E-10 -5.8150257E-10 1,midg,midg; igrid,midg,midg -7.9088298E-11 -6.3066502E-10 gauss-seidel spectral radius is 0.9823220 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 17:39:29 rms-change max change #iterations 7.7435859E-02 13.25494 at 10iterations 5.1260283E-03 0.8978710 at 20iterations 3.6348772E-04 6.3518524E-02 at 30iterations 4.9175251E-05 8.0404282E-03 at 40iterations 1.1761513E-05 2.0422935E-03 at 50iterations finished qdiffx linear iterations at : 17:39:32 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 1.1761513E-05 2.0422935E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 17:39:33 4.570u 0.388s 0:05.23 94.6% 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 Sat Oct 8 2011 at 17:39:33 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 = 3741 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.617594 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): -28.38700 33.46200 ymin,ymax (A): -34.11100 31.91300 zmin,zma (A): 9.104000 63.37600 x,y,z range (A): 61.84900 66.02400 54.27200 scale (grids/A): 1.617594 object centre (A): 2.537499 -1.099000 36.24000 number of atom coordinates read : 3741 total number of charged atoms : 3592 net assigned charge : -8.999979 assigned positive charge : 567.7997 centred at (gu) : 87.10596 90.98628 92.19332 assigned negative charge : -576.8017 centred at (gu) : 87.27175 91.03426 92.21767 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 76494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31288 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23767 mr = 52924 m= 2339 mr = 16439 m= 56 mr = 1113 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 129 time to turn everything in is 0.6400000 number of dielectric boundary points 32174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 359 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 27384 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) : 0.5391979 object centre at (A) : 2.537499 -1.099000 36.24000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1921706E-03 -7.7151302E-03 midg,1,midg; midg,igrid,midg -1.9979014E-03 -7.5951009E-03 1,midg,midg; igrid,midg,midg -1.8153397E-02 -2.7094042E-02 gauss-seidel spectral radius is 0.9982175 estimated iterations to convergence 188 setup time was (sec) 0.9600000 now iterating at: 17:39:34 rms-change max change #iterations 3.701146 171.0311 at 10iterations 1.556857 68.29664 at 20iterations 0.6534154 21.51106 at 30iterations 0.2752655 8.796507 at 40iterations 0.1152900 4.164434 at 50iterations 4.8724134E-02 1.695980 at 60iterations 2.0512830E-02 0.7110138 at 70iterations 8.6457096E-03 0.2788115 at 80iterations 3.6415707E-03 0.1190290 at 90iterations 1.5397256E-03 5.2520752E-02 at 100iterations 6.5251061E-04 2.0305634E-02 at 110iterations 2.7984293E-04 9.3917847E-03 at 120iterations finished qdiffx linear iterations at : 17:39:44 total time elapsed so far: 10.70000 # loops : 120 mean,max change (kT/e) : 2.7984293E-04 9.3917847E-03 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 17:39:45 10.867u 0.435s 0:11.56 97.6% 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 Sat Oct 8 2011 at 17:39:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3741 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.426390 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): -28.38700 33.46200 ymin,ymax (A): -34.11100 31.91300 zmin,zma (A): 9.104000 63.37600 x,y,z range (A): 61.84900 66.02400 54.27200 scale (grids/A): 2.426390 object centre (A): 2.537499 -1.099000 36.24000 number of atom coordinates read : 3741 total number of charged atoms : 3592 net assigned charge : -8.999979 assigned positive charge : 567.7997 centred at (gu) : 85.65870 91.47907 93.28970 assigned negative charge : -576.8017 centred at (gu) : 85.90749 91.55115 93.32645 start vw surface at 0.1400000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 178071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31288 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 82431 mr = 129664 m= 22997 mr = 65394 m= 3681 mr = 17322 m= 248 mr = 2321 m= 6 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 434 time to turn everything in is 1.570000 number of dielectric boundary points 72628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 28693 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) : 1.617594 object centre at (A) : 2.537499 -1.099000 36.24000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6084689E-02 -0.1389012 midg,1,midg; midg,igrid,midg -6.0321460E-03 -4.3192830E-02 1,midg,midg; igrid,midg,midg -0.3881712 -0.4013769 gauss-seidel spectral radius is 0.9991588 estimated iterations to convergence 272 setup time was (sec) 1.960000 now iterating at: 17:39:47 rms-change max change #iterations 9.687452 309.6436 at 10iterations 5.464656 119.2086 at 20iterations 3.072025 81.60511 at 30iterations 1.722393 32.56110 at 40iterations 0.9594802 18.41453 at 50iterations 0.5352206 12.39828 at 60iterations 0.2977185 5.900411 at 70iterations 0.1652183 3.239594 at 80iterations 9.1616146E-02 1.785909 at 90iterations 5.0877843E-02 1.011124 at 100iterations 2.8231382E-02 0.5886700 at 110iterations 1.5632398E-02 0.2956094 at 120iterations 8.6718472E-03 0.1887074 at 130iterations 4.8047197E-03 9.0305328E-02 at 140iterations 2.6624445E-03 6.3983440E-02 at 150iterations 1.4747134E-03 2.9113770E-02 at 160iterations 8.2079141E-04 1.4965057E-02 at 170iterations 4.5610470E-04 8.4590912E-03 at 180iterations finished qdiffx linear iterations at : 17:40:03 total time elapsed so far: 17.86000 # loops : 180 mean,max change (kT/e) : 4.5610470E-04 8.4590912E-03 energy calculations done at 17.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.03000 DelPhi exited at 17:40:03 18.036u 0.466s 0:18.83 98.1% 0+0k 0+0io 0pf+0w