Sat Oct 15 15:27:47 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 15 2011 at 15:27:47 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 = 3452 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: 0.5523319 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): -65.09900 -18.48100 ymin,ymax (A): -48.86500 10.66900 zmin,zma (A): -54.78100 9.672999 x,y,z range (A): 46.61800 59.53400 64.45400 scale (grids/A): 0.5523319 object centre (A): -41.79000 -19.09800 -22.55400 number of atom coordinates read : 3452 total number of charged atoms : 3295 net assigned charge : -4.500007 assigned positive charge : 527.3864 centred at (gu) : 90.03386 89.66486 91.85204 assigned negative charge : -531.8880 centred at (gu) : 89.81773 89.30841 91.94064 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6811 nv = 96 ne = 84 npr = 68813 no. pairs analyzed = 68813 no. exposed pairs = 4418 no. arc points = 31184 no. surface atoms = 1463 nbur = 1989 mkacc time = 0.1200000 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 = 1.540000 m= 267 mr = 3501 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2500000 number of dielectric boundary points 3569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3173 ## 416 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5077252E-10 -1.9213244E-09 midg,1,midg; midg,igrid,midg -4.3982111E-09 2.8489144E-09 1,midg,midg; igrid,midg,midg -2.5164364E-09 1.8049477E-09 gauss-seidel spectral radius is 0.9831319 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 15:27:47 rms-change max change #iterations 8.4463388E-02 13.27704 at 10iterations 6.1034630E-03 1.001787 at 20iterations 5.9196120E-04 9.2896461E-02 at 30iterations 1.1444705E-04 1.7768860E-02 at 40iterations 2.8681225E-05 4.2972565E-03 at 50iterations finished qdiffx linear iterations at : 15:27:51 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 2.8681225E-05 4.2972565E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 15:27:52 4.448u 0.320s 0:05.11 93.1% 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 15 2011 at 15:27:52 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 = 3452 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: 1.656996 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): -65.09900 -18.48100 ymin,ymax (A): -48.86500 10.66900 zmin,zma (A): -54.78100 9.672999 x,y,z range (A): 46.61800 59.53400 64.45400 scale (grids/A): 1.656996 object centre (A): -41.79000 -19.09800 -22.55400 number of atom coordinates read : 3452 total number of charged atoms : 3295 net assigned charge : -4.500007 assigned positive charge : 527.3864 centred at (gu) : 90.10033 88.99377 95.55523 assigned negative charge : -531.8880 centred at (gu) : 89.45288 87.92486 95.82174 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 75562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31184 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23889 mr = 51346 m= 2392 mr = 16317 m= 82 mr = 1112 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2457 time to turn everything in is 0.3900000 number of dielectric boundary points 33146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 25295 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) : 0.5523319 object centre at (A) : -41.79000 -19.09800 -22.55400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5317321E-02 -1.8990368E-02 midg,1,midg; midg,igrid,midg -5.2984145E-02 2.8406907E-02 1,midg,midg; igrid,midg,midg -9.1881622E-03 1.4619003E-02 gauss-seidel spectral radius is 0.9982919 estimated iterations to convergence 192 setup time was (sec) 0.6500000 now iterating at: 15:27:53 rms-change max change #iterations 3.798445 192.0472 at 10iterations 1.615369 62.41459 at 20iterations 0.6894131 23.99292 at 30iterations 0.2960467 9.949190 at 40iterations 0.1265916 4.256323 at 50iterations 5.4210167E-02 1.899769 at 60iterations 2.3233173E-02 0.7578028 at 70iterations 9.9698957E-03 0.3193550 at 80iterations 4.2834068E-03 0.1600158 at 90iterations 1.8485977E-03 6.0498714E-02 at 100iterations 8.0522557E-04 2.7091980E-02 at 110iterations 3.5445619E-04 1.2172699E-02 at 120iterations finished qdiffx linear iterations at : 15:28:04 total time elapsed so far: 9.060000 # loops : 120 mean,max change (kT/e) : 3.5445619E-04 1.2172699E-02 energy calculations done at 9.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.180000 DelPhi exited at 15:28:04 9.184u 0.300s 0:12.68 74.7% 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 Sat Oct 15 2011 at 15:28:04 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 = 3452 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: 2.485493 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): -65.09900 -18.48100 ymin,ymax (A): -48.86500 10.66900 zmin,zma (A): -54.78100 9.672999 x,y,z range (A): 46.61800 59.53400 64.45400 scale (grids/A): 2.485493 object centre (A): -41.79000 -19.09800 -22.55400 number of atom coordinates read : 3452 total number of charged atoms : 3295 net assigned charge : -4.500007 assigned positive charge : 527.3864 centred at (gu) : 90.15010 88.49040 98.33274 assigned negative charge : -531.8880 centred at (gu) : 89.17922 86.88717 98.73249 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 175219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31184 grid for indexing accessible points = 1.400000 m= 82398 mr = 125374 m= 23442 mr = 65200 m= 3722 mr = 17344 m= 304 mr = 2254 m= 11 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 7912 time to turn everything in is 0.9800000 number of dielectric boundary points 74793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 26341 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) : 1.656996 object centre at (A) : -41.79000 -19.09800 -22.55400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2034070 -0.2240732 midg,1,midg; midg,igrid,midg -0.7725517 0.3570738 1,midg,midg; igrid,midg,midg -5.9234135E-02 0.1889291 gauss-seidel spectral radius is 0.9991822 estimated iterations to convergence 276 setup time was (sec) 1.290000 now iterating at: 15:28:06 rms-change max change #iterations 9.703222 272.0220 at 10iterations 5.562808 138.3412 at 20iterations 3.153708 73.99426 at 30iterations 1.788748 42.33469 at 40iterations 1.009701 21.88954 at 50iterations 0.5698362 14.27019 at 60iterations 0.3201075 7.179320 at 70iterations 0.1797302 3.876457 at 80iterations 0.1010450 2.205755 at 90iterations 5.6648437E-02 1.046693 at 100iterations 3.1713877E-02 0.7335510 at 110iterations 1.7782314E-02 0.3608456 at 120iterations 9.9327313E-03 0.1941147 at 130iterations 5.5709155E-03 0.1106720 at 140iterations 3.1178726E-03 5.8120728E-02 at 150iterations 1.7478276E-03 3.7765503E-02 at 160iterations 9.8344358E-04 2.0001888E-02 at 170iterations 5.5541721E-04 1.0349274E-02 at 180iterations finished qdiffx linear iterations at : 15:28:20 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 5.5541721E-04 1.0349274E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.23000 DelPhi exited at 15:28:20 15.232u 0.301s 0:15.82 98.1% 0+0k 0+0io 0pf+0w