Sat Oct 15 11:52:57 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 11:52:57 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 = 2288 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: 0.6294869 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): -14.00300 40.16900 ymin,ymax (A): -30.98800 25.56600 zmin,zma (A): -9.690001 33.20300 x,y,z range (A): 54.17200 56.55400 42.89300 scale (grids/A): 0.6294869 object centre (A): 13.08300 -2.710999 11.75650 number of atom coordinates read : 2288 total number of charged atoms : 2154 net assigned charge : 10.00002 assigned positive charge : 331.1237 centred at (gu) : 89.49975 91.13865 91.12024 assigned negative charge : -321.1241 centred at (gu) : 89.53139 91.18982 91.03815 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6353 nv = 96 ne = 84 npr = 45029 no. pairs analyzed = 45029 no. exposed pairs = 3012 no. arc points = 22222 no. surface atoms = 1012 nbur = 1276 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3310 m= 5 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.1800000 number of dielectric boundary points 3366 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2140 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7489 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7720169E-09 2.0999893E-08 midg,1,midg; midg,igrid,midg 1.1247796E-08 8.7643786E-09 1,midg,midg; igrid,midg,midg 1.4361913E-08 7.5431270E-09 gauss-seidel spectral radius is 0.9869127 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 11:52:57 rms-change max change #iterations 0.1235899 19.69607 at 10iterations 1.1700007E-02 1.993484 at 20iterations 1.1122719E-03 0.1531906 at 30iterations 1.0467078E-04 1.7383575E-02 at 40iterations 1.0287627E-05 1.3999939E-03 at 50iterations finished qdiffx linear iterations at : 11:53:01 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 1.0287627E-05 1.3999939E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 11:53:01 3.989u 0.238s 0:04.56 92.3% 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 Sat Oct 15 2011 at 11:53:01 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 = 2288 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: 1.888461 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): -14.00300 40.16900 ymin,ymax (A): -30.98800 25.56600 zmin,zma (A): -9.690001 33.20300 x,y,z range (A): 54.17200 56.55400 42.89300 scale (grids/A): 1.888461 object centre (A): 13.08300 -2.710999 11.75650 number of atom coordinates read : 2288 total number of charged atoms : 2154 net assigned charge : 10.00002 assigned positive charge : 331.1237 centred at (gu) : 88.49912 93.41602 93.36062 assigned negative charge : -321.1241 centred at (gu) : 88.59424 93.56953 93.11449 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22222 grid for indexing accessible points = 1.400000 m= 23755 mr = 45745 m= 3723 mr = 16926 m= 259 mr = 2156 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3410 time to turn everything in is 0.3600000 number of dielectric boundary points 31198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16898 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) : 0.6294869 object centre at (A) : 13.08300 -2.710999 11.75650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0800727E-03 2.3576785E-02 midg,1,midg; midg,igrid,midg 4.7165699E-02 3.0026548E-02 1,midg,midg; igrid,midg,midg 3.6506172E-02 3.5943542E-02 gauss-seidel spectral radius is 0.9985930 estimated iterations to convergence 211 setup time was (sec) 0.6400000 now iterating at: 11:53:02 rms-change max change #iterations 3.765519 166.1815 at 10iterations 1.733929 71.23992 at 20iterations 0.8013435 27.96901 at 30iterations 0.3695071 12.75369 at 40iterations 0.1704839 5.066187 at 50iterations 7.9028413E-02 2.723105 at 60iterations 3.6388155E-02 1.215196 at 70iterations 1.6770277E-02 0.5248833 at 80iterations 7.8072157E-03 0.2629452 at 90iterations 3.5993147E-03 0.1211624 at 100iterations 1.6641421E-03 5.4208755E-02 at 110iterations 7.6872774E-04 2.5523424E-02 at 120iterations finished qdiffx linear iterations at : 11:53:13 total time elapsed so far: 8.950000 # loops : 120 mean,max change (kT/e) : 7.6872774E-04 2.5523424E-02 energy calculations done at 8.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.080000 DelPhi exited at 11:53:13 9.084u 0.306s 0:11.69 80.2% 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 11:53:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2288 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: 2.832691 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): -14.00300 40.16900 ymin,ymax (A): -30.98800 25.56600 zmin,zma (A): -9.690001 33.20300 x,y,z range (A): 54.17200 56.55400 42.89300 scale (grids/A): 2.832691 object centre (A): 13.08300 -2.710999 11.75650 number of atom coordinates read : 2288 total number of charged atoms : 2154 net assigned charge : 10.00002 assigned positive charge : 331.1237 centred at (gu) : 87.74860 95.12401 95.04079 assigned negative charge : -321.1241 centred at (gu) : 87.89134 95.35426 94.67168 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 158098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22222 grid for indexing accessible points = 1.400000 m= 77120 mr = 111268 m= 27297 mr = 61995 m= 6585 mr = 21137 m= 1011 mr = 4674 m= 55 mr = 635 m= 0 mr = 20 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 11085 time to turn everything in is 0.9400000 number of dielectric boundary points 70437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 17227 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) : 1.888461 object centre at (A) : 13.08300 -2.710999 11.75650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7526307E-02 0.2541973 midg,1,midg; midg,igrid,midg 0.7123935 0.4131280 1,midg,midg; igrid,midg,midg 0.3621653 0.3734878 gauss-seidel spectral radius is 0.9992514 estimated iterations to convergence 288 setup time was (sec) 1.250000 now iterating at: 11:53:15 rms-change max change #iterations 9.041645 524.6926 at 10iterations 5.296874 133.9463 at 20iterations 3.066781 74.38786 at 30iterations 1.777507 51.46803 at 40iterations 1.023661 23.79956 at 50iterations 0.5897870 13.28929 at 60iterations 0.3390174 6.727146 at 70iterations 0.1944980 4.048122 at 80iterations 0.1116259 2.479488 at 90iterations 6.3996114E-02 1.289805 at 100iterations 3.6648311E-02 0.8316269 at 110iterations 2.1029577E-02 0.4761658 at 120iterations 1.2022279E-02 0.2231016 at 130iterations 6.8644756E-03 0.1364212 at 140iterations 3.9364011E-03 7.4871451E-02 at 150iterations 2.2526556E-03 4.7527313E-02 at 160iterations 1.2890416E-03 2.5140762E-02 at 170iterations 7.3680747E-04 1.4207840E-02 at 180iterations finished qdiffx linear iterations at : 11:53:30 total time elapsed so far: 14.87000 # loops : 180 mean,max change (kT/e) : 7.3680747E-04 1.4207840E-02 energy calculations done at 14.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.00000 DelPhi exited at 11:53:31 15.002u 0.320s 0:17.49 87.5% 0+0k 0+0io 0pf+0w