Sat Oct 15 12:23:44 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 12:23:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2479 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5737309 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): -11.81200 37.10400 ymin,ymax (A): -28.46100 22.15600 zmin,zma (A): 31.84000 93.89000 x,y,z range (A): 48.91600 50.61700 62.05000 scale (grids/A): 0.5737309 object centre (A): 12.64600 -3.152500 62.86500 number of atom coordinates read : 2479 total number of charged atoms : 2343 net assigned charge : -4.999986 assigned positive charge : 329.9083 centred at (gu) : 91.47916 88.23290 91.06467 assigned negative charge : -334.9089 centred at (gu) : 91.42011 88.26395 91.34660 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5583 nv = 96 ne = 84 npr = 51431 no. pairs analyzed = 51431 no. exposed pairs = 3533 no. arc points = 25212 no. surface atoms = 1190 nbur = 1289 mkacc time = 9.0000004E-02 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 = 1.512000 m= 276 mr = 2549 m= 3 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2327 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6821 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1589548E-09 -6.1097958E-09 midg,1,midg; midg,igrid,midg -6.2936739E-10 -8.3594198E-10 1,midg,midg; igrid,midg,midg -1.1578064E-09 -6.1820556E-11 gauss-seidel spectral radius is 0.9842989 estimated iterations to convergence 66 setup time was (sec) 0.4200000 now iterating at: 12:23:45 rms-change max change #iterations 7.7960745E-02 14.57167 at 10iterations 5.8830474E-03 1.038078 at 20iterations 4.8641281E-04 8.0596924E-02 at 30iterations 6.2580584E-05 1.0787964E-02 at 40iterations 1.3516927E-05 2.1729469E-03 at 50iterations finished qdiffx linear iterations at : 12:23:49 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 1.3516927E-05 2.1729469E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 12:23:49 3.908u 0.241s 0:04.71 87.8% 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 12:23:49 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 = 2479 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.721193 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): -11.81200 37.10400 ymin,ymax (A): -28.46100 22.15600 zmin,zma (A): 31.84000 93.89000 x,y,z range (A): 48.91600 50.61700 62.05000 scale (grids/A): 1.721193 object centre (A): 12.64600 -3.152500 62.86500 number of atom coordinates read : 2479 total number of charged atoms : 2343 net assigned charge : -4.999986 assigned positive charge : 329.9083 centred at (gu) : 94.43725 84.69845 93.19344 assigned negative charge : -334.9089 centred at (gu) : 94.26037 84.79175 94.03954 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25212 grid for indexing accessible points = 1.400000 m= 19020 mr = 38414 m= 2327 mr = 12122 m= 78 mr = 1076 m= 1 mr = 14 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 0.3100000 number of dielectric boundary points 30493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 18230 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) : 0.5737309 object centre at (A) : 12.64600 -3.152500 62.86500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6934823E-02 -4.3938279E-02 midg,1,midg; midg,igrid,midg 2.4823239E-03 -1.3044863E-03 1,midg,midg; igrid,midg,midg -3.2298365E-03 -6.1348779E-04 gauss-seidel spectral radius is 0.9983472 estimated iterations to convergence 195 setup time was (sec) 0.5500000 now iterating at: 12:23:50 rms-change max change #iterations 3.186796 174.4223 at 10iterations 1.370204 65.13905 at 20iterations 0.5912902 23.66242 at 30iterations 0.2573799 10.10324 at 40iterations 0.1115028 4.227245 at 50iterations 4.8274614E-02 1.776814 at 60iterations 2.1020968E-02 0.7910206 at 70iterations 9.0995524E-03 0.3466363 at 80iterations 3.9361478E-03 0.1764688 at 90iterations 1.7109640E-03 6.4514160E-02 at 100iterations 7.4731786E-04 2.6802063E-02 at 110iterations 3.2301995E-04 1.2095451E-02 at 120iterations finished qdiffx linear iterations at : 12:23:58 total time elapsed so far: 8.620000 # loops : 120 mean,max change (kT/e) : 3.2301995E-04 1.2095451E-02 energy calculations done at 8.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.760000 DelPhi exited at 12:23:59 8.758u 0.268s 0:09.36 96.2% 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 12:23:59 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 = 2479 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.581789 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): -11.81200 37.10400 ymin,ymax (A): -28.46100 22.15600 zmin,zma (A): 31.84000 93.89000 x,y,z range (A): 48.91600 50.61700 62.05000 scale (grids/A): 2.581789 object centre (A): 12.64600 -3.152500 62.86500 number of atom coordinates read : 2479 total number of charged atoms : 2343 net assigned charge : -4.999986 assigned positive charge : 329.9083 centred at (gu) : 96.65578 82.04751 94.79012 assigned negative charge : -334.9089 centred at (gu) : 96.39064 82.18765 96.05936 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 140561 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25212 grid for indexing accessible points = 1.400000 m= 63120 mr = 94719 m= 19719 mr = 47527 m= 3685 mr = 13941 m= 329 mr = 2288 m= 4 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 68795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 18730 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) : 1.721193 object centre at (A) : 12.64600 -3.152500 62.86500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3428040 -0.5291759 midg,1,midg; midg,igrid,midg 3.5075016E-02 1.3100526E-03 1,midg,midg; igrid,midg,midg -1.2169225E-02 6.1931917E-03 gauss-seidel spectral radius is 0.9991924 estimated iterations to convergence 278 setup time was (sec) 1.080000 now iterating at: 12:24:00 rms-change max change #iterations 8.109076 275.3499 at 10iterations 4.703349 147.0824 at 20iterations 2.702120 82.21641 at 30iterations 1.541434 39.26539 at 40iterations 0.8735449 20.88610 at 50iterations 0.4963992 11.89475 at 60iterations 0.2805207 7.490393 at 70iterations 0.1580179 3.991377 at 80iterations 8.9075409E-02 2.089836 at 90iterations 5.0051093E-02 1.103645 at 100iterations 2.8205482E-02 0.6465111 at 110iterations 1.5802963E-02 0.3289289 at 120iterations 8.8782059E-03 0.2079773 at 130iterations 4.9878452E-03 0.1018677 at 140iterations 2.8027894E-03 6.0893059E-02 at 150iterations 1.5746749E-03 3.5526276E-02 at 160iterations 8.8482798E-04 1.8299103E-02 at 170iterations 4.9985340E-04 1.0564804E-02 at 180iterations finished qdiffx linear iterations at : 12:24:13 total time elapsed so far: 14.34000 # loops : 180 mean,max change (kT/e) : 4.9985340E-04 1.0564804E-02 energy calculations done at 14.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.47000 DelPhi exited at 12:24:14 14.475u 0.304s 0:15.14 97.5% 0+0k 0+0io 0pf+0w