Sat Oct 8 23:21:08 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 23:21:08 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2484 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6396551 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): 12.84100 67.18800 ymin,ymax (A): -30.30700 25.34800 zmin,zma (A): -9.624001 32.53400 x,y,z range (A): 54.34700 55.65500 42.15800 scale (grids/A): 0.6396551 object centre (A): 40.01450 -2.479500 11.45500 number of atom coordinates read : 2484 total number of charged atoms : 2345 net assigned charge : 11.50002 assigned positive charge : 361.6190 centred at (gu) : 89.89761 91.03003 90.75680 assigned negative charge : -350.1199 centred at (gu) : 89.87956 91.06290 90.69999 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7000 nv = 96 ne = 84 npr = 49727 no. pairs analyzed = 49727 no. exposed pairs = 3335 no. arc points = 23722 no. surface atoms = 1103 nbur = 1381 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 3668 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.3000000 number of dielectric boundary points 3697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8294 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1132568E-09 2.6300654E-08 midg,1,midg; midg,igrid,midg 1.6119142E-08 1.6189730E-08 1,midg,midg; igrid,midg,midg 1.4975891E-08 1.8034177E-08 gauss-seidel spectral radius is 0.9873373 estimated iterations to convergence 73 setup time was (sec) 0.5200000 now iterating at: 23:21:08 rms-change max change #iterations 0.1371792 19.08116 at 10iterations 1.3676676E-02 1.940666 at 20iterations 1.4805587E-03 0.2417603 at 30iterations 2.6982004E-04 5.0788879E-02 at 40iterations 8.5794985E-05 1.8152237E-02 at 50iterations finished qdiffx linear iterations at : 23:21:11 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 8.5794985E-05 1.8152237E-02 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 23:21:11 3.173u 0.156s 0:03.63 91.4% 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 23:21:11 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2484 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: 1.918965 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): 12.84100 67.18800 ymin,ymax (A): -30.30700 25.34800 zmin,zma (A): -9.624001 32.53400 x,y,z range (A): 54.34700 55.65500 42.15800 scale (grids/A): 1.918965 object centre (A): 40.01450 -2.479500 11.45500 number of atom coordinates read : 2484 total number of charged atoms : 2345 net assigned charge : 11.50002 assigned positive charge : 361.6190 centred at (gu) : 89.69239 93.08976 92.27000 assigned negative charge : -350.1199 centred at (gu) : 89.63863 93.18856 92.10011 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23722 grid for indexing accessible points = 1.400000 m= 26808 mr = 50745 m= 4116 mr = 19132 m= 269 mr = 2427 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 821 time to turn everything in is 0.5200000 number of dielectric boundary points 34164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 18479 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) : 0.6396551 object centre at (A) : 40.01450 -2.479500 11.45500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5262100E-03 3.3194005E-02 midg,1,midg; midg,igrid,midg 4.7423106E-02 2.9316433E-02 1,midg,midg; igrid,midg,midg 4.9403969E-02 5.6133892E-02 gauss-seidel spectral radius is 0.9986562 estimated iterations to convergence 216 setup time was (sec) 0.7900000 now iterating at: 23:21:12 rms-change max change #iterations 4.068331 164.5278 at 10iterations 1.911934 70.01259 at 20iterations 0.9000002 29.20127 at 30iterations 0.4209285 13.21856 at 40iterations 0.1989330 7.306992 at 50iterations 9.3573496E-02 2.797148 at 60iterations 4.3963082E-02 1.388361 at 70iterations 2.0642519E-02 0.6732917 at 80iterations 9.7952280E-03 0.3159294 at 90iterations 4.6309028E-03 0.1381044 at 100iterations 2.2125463E-03 6.5687180E-02 at 110iterations 1.0713853E-03 3.5358906E-02 at 120iterations finished qdiffx linear iterations at : 23:21:18 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 1.0713853E-03 3.5358906E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 23:21:19 6.892u 0.168s 0:07.33 96.1% 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 23:21:19 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2484 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: 2.878448 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): 12.84100 67.18800 ymin,ymax (A): -30.30700 25.34800 zmin,zma (A): -9.624001 32.53400 x,y,z range (A): 54.34700 55.65500 42.15800 scale (grids/A): 2.878448 object centre (A): 40.01450 -2.479500 11.45500 number of atom coordinates read : 2484 total number of charged atoms : 2345 net assigned charge : 11.50002 assigned positive charge : 361.6190 centred at (gu) : 89.53846 94.63461 93.40489 assigned negative charge : -350.1199 centred at (gu) : 89.45789 94.78290 93.15013 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 174106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23722 grid for indexing accessible points = 1.400000 m= 86211 mr = 123331 m= 30891 mr = 69212 m= 7508 mr = 24105 m= 1194 mr = 5456 m= 82 mr = 764 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 2734 time to turn everything in is 1.300000 number of dielectric boundary points 77078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18760 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) : 1.918965 object centre at (A) : 40.01450 -2.479500 11.45500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3757158E-02 0.3570209 midg,1,midg; midg,igrid,midg 0.6121972 0.3773278 1,midg,midg; igrid,midg,midg 0.5039436 0.5873286 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.570000 now iterating at: 23:21:21 rms-change max change #iterations 9.676332 380.7798 at 10iterations 5.746638 133.0574 at 20iterations 3.368107 77.23885 at 30iterations 1.968092 42.00207 at 40iterations 1.152766 25.80764 at 50iterations 0.6724084 13.24194 at 60iterations 0.3912725 7.675166 at 70iterations 0.2272223 4.333909 at 80iterations 0.1319549 2.455948 at 90iterations 7.6239966E-02 1.619422 at 100iterations 4.4277519E-02 0.8787613 at 110iterations 2.5582885E-02 0.4816284 at 120iterations 1.4811925E-02 0.2889151 at 130iterations 8.5918577E-03 0.1584625 at 140iterations 4.9814992E-03 9.7063065E-02 at 150iterations 2.9049220E-03 6.2255383E-02 at 160iterations 1.7031837E-03 3.1265259E-02 at 170iterations 1.0128609E-03 2.4688721E-02 at 180iterations finished qdiffx linear iterations at : 23:21:30 total time elapsed so far: 10.88000 # loops : 180 mean,max change (kT/e) : 1.0128609E-03 2.4688721E-02 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 23:21:30 11.060u 0.174s 0:11.50 97.6% 0+0k 0+0io 0pf+0w