Tue Oct 11 06:16:22 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 Tue Oct 11 2011 at 06:16:22 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 = 2125 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6845627 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): 15.67100 62.80700 ymin,ymax (A): -3.493000 33.73000 zmin,zma (A): 19.96800 71.97200 x,y,z range (A): 47.13600 37.22300 52.00400 scale (grids/A): 0.6845627 object centre (A): 39.23900 15.11850 45.97000 number of atom coordinates read : 2125 total number of charged atoms : 1997 net assigned charge : 6.500009 assigned positive charge : 324.3239 centred at (gu) : 91.42581 89.58458 89.02785 assigned negative charge : -317.8241 centred at (gu) : 91.54546 89.61147 88.94798 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6692 nv = 96 ne = 84 npr = 42449 no. pairs analyzed = 42449 no. exposed pairs = 2600 no. arc points = 17748 no. surface atoms = 888 nbur = 1237 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 3796 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1762 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7623 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6452784E-09 4.5854204E-08 midg,1,midg; midg,igrid,midg 4.3464059E-08 2.2290980E-08 1,midg,midg; igrid,midg,midg 5.0588355E-08 -5.8011862E-09 gauss-seidel spectral radius is 0.9888868 estimated iterations to convergence 77 setup time was (sec) 0.5900000 now iterating at: 06:16:23 rms-change max change #iterations 0.1746362 26.79324 at 10iterations 2.0334758E-02 2.734049 at 20iterations 2.5197805E-03 0.3998146 at 30iterations 4.1854664E-04 5.8761120E-02 at 40iterations 1.1268613E-04 1.7759323E-02 at 50iterations finished qdiffx linear iterations at : 06:16:27 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 1.1268613E-04 1.7759323E-02 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 06:16:28 4.967u 0.449s 0:05.79 93.2% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 06:16:28 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 = 2125 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.053688 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): 15.67100 62.80700 ymin,ymax (A): -3.493000 33.73000 zmin,zma (A): 19.96800 71.97200 x,y,z range (A): 47.13600 37.22300 52.00400 scale (grids/A): 2.053688 object centre (A): 39.23900 15.11850 45.97000 number of atom coordinates read : 2125 total number of charged atoms : 1997 net assigned charge : 6.500009 assigned positive charge : 324.3239 centred at (gu) : 94.27700 88.75376 87.08318 assigned negative charge : -317.8241 centred at (gu) : 94.63667 88.83446 86.84412 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17748 grid for indexing accessible points = 1.400000 m= 27795 mr = 50256 m= 4955 mr = 20943 m= 417 mr = 3226 m= 5 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 29882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15830 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) : 0.6845627 object centre at (A) : 39.23900 15.11850 45.97000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7509654E-02 4.5630526E-02 midg,1,midg; midg,igrid,midg 2.3210887E-02 9.4570825E-03 1,midg,midg; igrid,midg,midg 2.5342654E-02 1.7282464E-02 gauss-seidel spectral radius is 0.9987636 estimated iterations to convergence 225 setup time was (sec) 0.9400000 now iterating at: 06:16:29 rms-change max change #iterations 4.367843 182.9004 at 10iterations 2.121863 74.14323 at 20iterations 1.029537 35.14199 at 30iterations 0.5036797 16.44983 at 40iterations 0.2452735 7.522507 at 50iterations 0.1189268 4.084138 at 60iterations 5.7949491E-02 2.102913 at 70iterations 2.8216830E-02 0.8682404 at 80iterations 1.3858529E-02 0.4263243 at 90iterations 6.7862524E-03 0.2025795 at 100iterations 3.3403055E-03 9.5672607E-02 at 110iterations 1.6858258E-03 6.5148592E-02 at 120iterations finished qdiffx linear iterations at : 06:16:40 total time elapsed so far: 11.63000 # loops : 120 mean,max change (kT/e) : 1.6858258E-03 6.5148592E-02 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 06:16:40 11.819u 0.489s 0:12.60 97.5% 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 Tue Oct 11 2011 at 06:16:40 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 = 2125 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.080532 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): 15.67100 62.80700 ymin,ymax (A): -3.493000 33.73000 zmin,zma (A): 19.96800 71.97200 x,y,z range (A): 47.13600 37.22300 52.00400 scale (grids/A): 3.080532 object centre (A): 39.23900 15.11850 45.97000 number of atom coordinates read : 2125 total number of charged atoms : 1997 net assigned charge : 6.500009 assigned positive charge : 324.3239 centred at (gu) : 96.41562 88.13057 85.62478 assigned negative charge : -317.8241 centred at (gu) : 96.95478 88.25168 85.26612 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 164445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17748 grid for indexing accessible points = 1.400000 m= 88126 mr = 121292 m= 34125 mr = 73041 m= 9207 mr = 27816 m= 1673 mr = 6980 m= 170 mr = 1227 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.9999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 67299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 15976 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) : 2.053688 object centre at (A) : 39.23900 15.11850 45.97000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2843271 0.3620097 midg,1,midg; midg,igrid,midg 0.2169225 7.0745341E-02 1,midg,midg; igrid,midg,midg 0.2228869 0.4149176 gauss-seidel spectral radius is 0.9992819 estimated iterations to convergence 294 setup time was (sec) 2.220000 now iterating at: 06:16:43 rms-change max change #iterations 9.937354 424.5404 at 10iterations 5.821847 122.6331 at 20iterations 3.427056 78.10719 at 30iterations 2.008482 42.50062 at 40iterations 1.174810 24.76199 at 50iterations 0.6864061 13.85229 at 60iterations 0.4007344 7.723322 at 70iterations 0.2335158 4.420074 at 80iterations 0.1361582 2.526363 at 90iterations 7.9168163E-02 1.518185 at 100iterations 4.6232291E-02 0.8745356 at 110iterations 2.7074408E-02 0.5778198 at 120iterations 1.5928142E-02 0.3003008 at 130iterations 9.4645685E-03 0.1950798 at 140iterations 5.7436577E-03 0.1071396 at 150iterations 3.5866243E-03 6.8357468E-02 at 160iterations 2.3516044E-03 4.2586803E-02 at 170iterations 1.6326248E-03 3.1259537E-02 at 180iterations finished qdiffx linear iterations at : 06:17:01 total time elapsed so far: 19.89000 # loops : 180 mean,max change (kT/e) : 1.6326248E-03 3.1259537E-02 energy calculations done at 19.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.05000 DelPhi exited at 06:17:01 20.058u 0.540s 0:20.89 98.5% 0+0k 0+0io 0pf+0w