Sat Oct 15 11:53:31 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 Sat Oct 15 2011 at 11:53:31 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2288 !!! WARNING: HIT 84 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= 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 : 10.01402 assigned positive charge : 335.9656 centred at (gu) : 89.47822 91.06071 91.09798 assigned negative charge : -325.9521 centred at (gu) : 89.50882 91.11062 91.01249 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-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 3.5265211E-09 2.1338934E-08 midg,1,midg; midg,igrid,midg 1.1414325E-08 8.6845873E-09 1,midg,midg; igrid,midg,midg 1.4394571E-08 7.5565483E-09 gauss-seidel spectral radius is 0.9869127 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 11:53:32 rms-change max change #iterations 0.1269590 19.77667 at 10iterations 1.2052930E-02 1.950073 at 20iterations 1.1446743E-03 0.1637249 at 30iterations 1.0736710E-04 1.8127441E-02 at 40iterations 1.0589054E-05 1.4820099E-03 at 50iterations finished qdiffx linear iterations at : 11:53:35 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 1.0589054E-05 1.4820099E-03 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.920000 DelPhi exited at 11:53:35 3.919u 0.238s 0:04.52 91.5% 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 Sat Oct 15 2011 at 11:53:35 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2288 !!! WARNING: HIT 84 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= 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 : 10.01402 assigned positive charge : 335.9656 centred at (gu) : 88.43446 93.18212 93.29388 assigned negative charge : -325.9521 centred at (gu) : 88.52651 93.33189 93.03745 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 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 = 0.1700000 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 -5.0133863E-03 2.4552047E-02 midg,1,midg; midg,igrid,midg 4.6774559E-02 2.9803300E-02 1,midg,midg; igrid,midg,midg 3.6737721E-02 3.5286326E-02 gauss-seidel spectral radius is 0.9985930 estimated iterations to convergence 211 setup time was (sec) 0.6400000 now iterating at: 11:53:36 rms-change max change #iterations 3.844967 166.1817 at 10iterations 1.771498 71.30808 at 20iterations 0.8191231 27.96898 at 30iterations 0.3779090 12.74317 at 40iterations 0.1741694 5.390663 at 50iterations 8.0768757E-02 2.714063 at 60iterations 3.7166972E-02 1.226758 at 70iterations 1.7143071E-02 0.5602627 at 80iterations 7.9770153E-03 0.2605444 at 90iterations 3.6788878E-03 0.1287832 at 100iterations 1.6996177E-03 5.6385040E-02 at 110iterations 7.8614859E-04 2.6756287E-02 at 120iterations finished qdiffx linear iterations at : 11:53:47 total time elapsed so far: 8.830000 # loops : 120 mean,max change (kT/e) : 7.8614859E-04 2.6756287E-02 energy calculations done at 8.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 11:53:47 8.969u 0.301s 0:11.74 78.8% 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 11:53:47 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2288 !!! WARNING: HIT 84 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= 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 : 10.01402 assigned positive charge : 335.9656 centred at (gu) : 87.65158 94.77320 94.94066 assigned negative charge : -325.9521 centred at (gu) : 87.78976 94.99780 94.55617 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 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 = 0.5300000 no. cavity mid-points inaccessible to solvent = 11085 time to turn everything in is 0.9800000 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 1.110000 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 -4.4917416E-02 0.2642047 midg,1,midg; midg,igrid,midg 0.7036899 0.4109890 1,midg,midg; igrid,midg,midg 0.3681902 0.3647229 gauss-seidel spectral radius is 0.9992514 estimated iterations to convergence 288 setup time was (sec) 1.310000 now iterating at: 11:53:49 rms-change max change #iterations 9.205308 524.6926 at 10iterations 5.389131 133.9464 at 20iterations 3.118701 74.24891 at 30iterations 1.806636 51.53574 at 40iterations 1.040203 23.85365 at 50iterations 0.5992479 13.27623 at 60iterations 0.3443874 6.590047 at 70iterations 0.1974786 3.994759 at 80iterations 0.1133196 2.517475 at 90iterations 6.4945988E-02 1.290215 at 100iterations 3.7196215E-02 0.8598938 at 110iterations 2.1344749E-02 0.4697609 at 120iterations 1.2198800E-02 0.2250109 at 130iterations 6.9656800E-03 0.1356163 at 140iterations 3.9934353E-03 7.7072144E-02 at 150iterations 2.2853517E-03 4.7214508E-02 at 160iterations 1.3074895E-03 2.5634766E-02 at 170iterations 7.4769370E-04 1.4547348E-02 at 180iterations finished qdiffx linear iterations at : 11:54:13 total time elapsed so far: 14.17000 # loops : 180 mean,max change (kT/e) : 7.4769370E-04 1.4547348E-02 energy calculations done at 14.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.31000 DelPhi exited at 11:54:14 14.313u 0.346s 0:26.24 55.8% 0+0k 0+0io 0pf+0w