Mon Oct 10 19:20:45 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 Mon Oct 10 2011 at 19:20:45 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2349 !!! WARNING: HIR 440 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6087551 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): -18.37000 33.37100 ymin,ymax (A): -21.07800 23.85900 zmin,zma (A): -30.25000 28.23000 x,y,z range (A): 51.74100 44.93700 58.48000 scale (grids/A): 0.6087551 object centre (A): 7.500502 1.390500 -1.010000 number of atom coordinates read : 2349 total number of charged atoms : 2214 net assigned charge : -1.985994 assigned positive charge : 344.8483 centred at (gu) : 90.08362 90.27197 90.16251 assigned negative charge : -346.8350 centred at (gu) : 90.06073 90.24715 90.20117 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5730 nv = 96 ne = 84 npr = 47987 no. pairs analyzed = 47987 no. exposed pairs = 3069 no. arc points = 21112 no. surface atoms = 1055 nbur = 1294 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 3000 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2087 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9191007E-10 -2.8871761E-09 midg,1,midg; midg,igrid,midg -2.0616500E-09 -7.3738425E-11 1,midg,midg; igrid,midg,midg -2.0682163E-09 -1.5697008E-10 gauss-seidel spectral radius is 0.9860116 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 19:20:46 rms-change max change #iterations 0.1100556 16.98843 at 10iterations 9.3836803E-03 1.404560 at 20iterations 8.6037308E-04 0.1205750 at 30iterations 8.2184582E-05 1.3439655E-02 at 40iterations 1.4449318E-05 3.2279491E-03 at 50iterations finished qdiffx linear iterations at : 19:20:49 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.4449318E-05 3.2279491E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 19:20:49 3.599u 0.198s 0:04.31 87.7% 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 Mon Oct 10 2011 at 19:20:50 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2349 !!! WARNING: HIR 440 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.826265 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): -18.37000 33.37100 ymin,ymax (A): -21.07800 23.85900 zmin,zma (A): -30.25000 28.23000 x,y,z range (A): 51.74100 44.93700 58.48000 scale (grids/A): 1.826265 object centre (A): 7.500502 1.390500 -1.010000 number of atom coordinates read : 2349 total number of charged atoms : 2214 net assigned charge : -1.985994 assigned positive charge : 344.8483 centred at (gu) : 90.25045 90.81544 90.48681 assigned negative charge : -346.8350 centred at (gu) : 90.18198 90.74129 90.60359 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21112 grid for indexing accessible points = 1.400000 m= 21171 mr = 42142 m= 3293 mr = 14952 m= 166 mr = 1916 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 27903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17343 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) : 0.6087551 object centre at (A) : 7.500502 1.390500 -1.010000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2578029E-02 -4.0726833E-02 midg,1,midg; midg,igrid,midg 4.7530004E-04 -6.0579629E-04 1,midg,midg; igrid,midg,midg -1.5304457E-02 1.6167814E-02 gauss-seidel spectral radius is 0.9984952 estimated iterations to convergence 204 setup time was (sec) 0.8100000 now iterating at: 19:20:51 rms-change max change #iterations 3.664719 197.8192 at 10iterations 1.644881 70.11799 at 20iterations 0.7386391 25.25789 at 30iterations 0.3340728 12.47543 at 40iterations 0.1503923 5.724544 at 50iterations 6.7768373E-02 2.252352 at 60iterations 3.0419976E-02 1.022698 at 70iterations 1.3733419E-02 0.5073242 at 80iterations 6.1922842E-03 0.2302418 at 90iterations 2.7964534E-03 9.9788666E-02 at 100iterations 1.2649370E-03 4.6662331E-02 at 110iterations 5.7558395E-04 2.1728992E-02 at 120iterations finished qdiffx linear iterations at : 19:20:57 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 5.7558395E-04 2.1728992E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 19:20:58 7.959u 0.234s 0:08.67 94.3% 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 Mon Oct 10 2011 at 19:20:58 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2349 !!! WARNING: HIR 440 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.739398 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): -18.37000 33.37100 ymin,ymax (A): -21.07800 23.85900 zmin,zma (A): -30.25000 28.23000 x,y,z range (A): 51.74100 44.93700 58.48000 scale (grids/A): 2.739398 object centre (A): 7.500502 1.390500 -1.010000 number of atom coordinates read : 2349 total number of charged atoms : 2214 net assigned charge : -1.985994 assigned positive charge : 344.8483 centred at (gu) : 90.37544 91.22314 90.73020 assigned negative charge : -346.8350 centred at (gu) : 90.27309 91.11185 90.90540 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 144747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21112 grid for indexing accessible points = 1.400000 m= 68597 mr = 103171 m= 24295 mr = 54630 m= 5871 mr = 18922 m= 802 mr = 4257 m= 28 mr = 486 m= 0 mr = 8 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 62866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 17711 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) : 1.826265 object centre at (A) : 7.500502 1.390500 -1.010000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4804602 -0.6724713 midg,1,midg; midg,igrid,midg -1.1948775E-02 -4.6240203E-02 1,midg,midg; igrid,midg,midg -0.2634343 0.2462708 gauss-seidel spectral radius is 0.9992170 estimated iterations to convergence 282 setup time was (sec) 1.560000 now iterating at: 19:21:00 rms-change max change #iterations 8.902576 416.0954 at 10iterations 5.143897 121.8348 at 20iterations 2.949362 64.71219 at 30iterations 1.691093 37.67041 at 40iterations 0.9668031 24.27637 at 50iterations 0.5493689 11.28013 at 60iterations 0.3127226 6.914021 at 70iterations 0.1777708 3.925814 at 80iterations 0.1008669 2.066284 at 90iterations 5.7182491E-02 1.141356 at 100iterations 3.2472458E-02 0.6519032 at 110iterations 1.8404339E-02 0.3618412 at 120iterations 1.0427927E-02 0.2115469 at 130iterations 5.9245862E-03 0.1278000 at 140iterations 3.3693011E-03 7.4518204E-02 at 150iterations 1.9270862E-03 3.9538383E-02 at 160iterations 1.1116563E-03 2.4207115E-02 at 170iterations 6.5123365E-04 1.4185190E-02 at 180iterations finished qdiffx linear iterations at : 19:21:11 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 6.5123365E-04 1.4185190E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 19:21:11 12.369u 0.263s 0:13.15 95.9% 0+0k 0+0io 0pf+0w