Mon Oct 10 17:06:00 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 17:06:00 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1837 !!! WARNING: HIT 148 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7114450 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): -26.33700 23.08600 ymin,ymax (A): -2.955000 38.19600 zmin,zma (A): 25.30900 75.34800 x,y,z range (A): 49.42300 41.15100 50.03900 scale (grids/A): 0.7114450 object centre (A): -1.625500 17.62050 50.32850 number of atom coordinates read : 1837 total number of charged atoms : 1708 net assigned charge : -5.485985 assigned positive charge : 267.2643 centred at (gu) : 88.00063 90.41209 91.33554 assigned negative charge : -272.7501 centred at (gu) : 88.06676 90.46642 91.42074 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6402 nv = 96 ne = 84 npr = 38219 no. pairs analyzed = 38219 no. exposed pairs = 2357 no. arc points = 17283 no. surface atoms = 799 nbur = 1038 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3398 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.1600000 number of dielectric boundary points 3343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1471 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9299723E-09 -1.1767518E-07 midg,1,midg; midg,igrid,midg -2.3378945E-08 -8.2392120E-08 1,midg,midg; igrid,midg,midg -2.7568106E-08 -5.6018042E-08 gauss-seidel spectral radius is 0.9896894 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 17:06:01 rms-change max change #iterations 0.1970304 29.64829 at 10iterations 2.3846749E-02 3.619257 at 20iterations 2.9064815E-03 0.4275646 at 30iterations 3.6708437E-04 5.1010132E-02 at 40iterations 4.5346740E-05 6.2408447E-03 at 50iterations finished qdiffx linear iterations at : 17:06:04 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.5346740E-05 6.2408447E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 17:06:05 3.354u 0.162s 0:04.13 84.9% 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 17:06:05 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1837 !!! WARNING: HIT 148 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.134335 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): -26.33700 23.08600 ymin,ymax (A): -2.955000 38.19600 zmin,zma (A): 25.30900 75.34800 x,y,z range (A): 49.42300 41.15100 50.03900 scale (grids/A): 2.134335 object centre (A): -1.625500 17.62050 50.32850 number of atom coordinates read : 1837 total number of charged atoms : 1708 net assigned charge : -5.485985 assigned positive charge : 267.2643 centred at (gu) : 84.00185 91.23643 94.00679 assigned negative charge : -272.7501 centred at (gu) : 84.20037 91.39935 94.26225 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 67950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17283 grid for indexing accessible points = 1.400000 m= 23930 mr = 45478 m= 4219 mr = 17294 m= 360 mr = 2710 m= 7 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 426 time to turn everything in is 0.3300000 number of dielectric boundary points 30794 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13585 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) : 0.7114450 object centre at (A) : -1.625500 17.62050 50.32850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1059590 -8.1654765E-02 midg,1,midg; midg,igrid,midg -1.6492407E-03 -1.9752312E-02 1,midg,midg; igrid,midg,midg 3.6182318E-02 1.8566094E-02 gauss-seidel spectral radius is 0.9988353 estimated iterations to convergence 232 setup time was (sec) 0.5500000 now iterating at: 17:06:06 rms-change max change #iterations 4.387431 205.4202 at 10iterations 2.160058 73.04951 at 20iterations 1.069207 38.85227 at 30iterations 0.5289407 16.60522 at 40iterations 0.2623733 9.358704 at 50iterations 0.1302555 4.415579 at 60iterations 6.4564496E-02 1.957095 at 70iterations 3.1978551E-02 0.9646416 at 80iterations 1.5796328E-02 0.5447893 at 90iterations 7.8268424E-03 0.2545652 at 100iterations 3.8740402E-03 0.1234808 at 110iterations 1.9299515E-03 6.2505722E-02 at 120iterations finished qdiffx linear iterations at : 17:06:13 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.9299515E-03 6.2505722E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 17:06:13 7.750u 0.206s 0:08.30 95.7% 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 17:06:13 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1837 !!! WARNING: HIT 148 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.201503 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): -26.33700 23.08600 ymin,ymax (A): -2.955000 38.19600 zmin,zma (A): 25.30900 75.34800 x,y,z range (A): 49.42300 41.15100 50.03900 scale (grids/A): 3.201503 object centre (A): -1.625500 17.62050 50.32850 number of atom coordinates read : 1837 total number of charged atoms : 1708 net assigned charge : -5.485985 assigned positive charge : 267.2643 centred at (gu) : 81.00287 91.85468 96.01034 assigned negative charge : -272.7501 centred at (gu) : 81.30059 92.09905 96.39341 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 156901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17283 grid for indexing accessible points = 1.400000 m= 76207 mr = 110295 m= 28726 mr = 61451 m= 7790 mr = 22961 m= 1450 mr = 5921 m= 143 mr = 1037 m= 3 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 1414 time to turn everything in is 1.030000 number of dielectric boundary points 69466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 13664 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) : 2.134335 object centre at (A) : -1.625500 17.62050 50.32850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.099842 -0.7053401 midg,1,midg; midg,igrid,midg -1.1354577E-02 -0.1306645 1,midg,midg; igrid,midg,midg 0.2771210 0.2824968 gauss-seidel spectral radius is 0.9993060 estimated iterations to convergence 299 setup time was (sec) 1.270000 now iterating at: 17:06:15 rms-change max change #iterations 9.742259 327.3826 at 10iterations 5.737495 136.2658 at 20iterations 3.368534 71.55946 at 30iterations 1.979124 46.79057 at 40iterations 1.159011 22.00509 at 50iterations 0.6812982 12.94596 at 60iterations 0.3982230 8.034718 at 70iterations 0.2332046 4.345474 at 80iterations 0.1361587 2.431908 at 90iterations 7.9662152E-02 1.566093 at 100iterations 4.6522830E-02 0.8662157 at 110iterations 2.7204962E-02 0.5012531 at 120iterations 1.5867675E-02 0.2934055 at 130iterations 9.3105910E-03 0.1994953 at 140iterations 5.4278378E-03 9.7244263E-02 at 150iterations 3.1751303E-03 5.9413910E-02 at 160iterations 1.8564163E-03 3.4599304E-02 at 170iterations 1.0857651E-03 2.1183014E-02 at 180iterations finished qdiffx linear iterations at : 17:06:26 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 1.0857651E-03 2.1183014E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 17:06:27 12.713u 0.189s 0:13.34 96.6% 0+0k 0+0io 0pf+0w