Tue Nov 22 14:11:21 PST 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 Tue Nov 22 2011 at 14:11:25 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 0.6554238 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): -4.297000 34.33100 ymin,ymax (A): -3.440000 48.11900 zmin,zma (A): -23.48600 30.83000 x,y,z range (A): 38.62800 51.55900 54.31600 scale (grids/A): 0.6554238 object centre (A): 15.01700 22.33950 3.672000 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 293.1439 centred at (gu) : 90.29908 92.58994 90.03014 assigned negative charge : -290.1442 centred at (gu) : 90.39990 92.71716 89.97048 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5693 nv = 96 ne = 84 npr = 40318 no. pairs analyzed = 40318 no. exposed pairs = 2520 no. arc points = 17340 no. surface atoms = 854 nbur = 1106 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3135 m= 0 mr = 49 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.1700000 number of dielectric boundary points 2834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1671 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6657 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8988231E-10 1.5050915E-08 midg,1,midg; midg,igrid,midg 1.3804108E-08 -1.7195456E-08 1,midg,midg; igrid,midg,midg 1.9004847E-08 -6.4814900E-09 gauss-seidel spectral radius is 0.9878771 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 14:11:28 rms-change max change #iterations 0.1409630 22.23915 at 10iterations 1.4596206E-02 2.345547 at 20iterations 1.5321882E-03 0.2647285 at 30iterations 1.5729992E-04 2.5283813E-02 at 40iterations 1.6419386E-05 2.4375916E-03 at 50iterations finished qdiffx linear iterations at : 14:11:38 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 1.6419386E-05 2.4375916E-03 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 14:11:40 3.787u 0.217s 0:15.42 25.8% 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 Tue Nov 22 2011 at 14:11:44 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 1.966271 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): -4.297000 34.33100 ymin,ymax (A): -3.440000 48.11900 zmin,zma (A): -23.48600 30.83000 x,y,z range (A): 38.62800 51.55900 54.31600 scale (grids/A): 1.966271 object centre (A): 15.01700 22.33950 3.672000 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 293.1439 centred at (gu) : 90.89721 97.76993 90.09039 assigned negative charge : -290.1442 centred at (gu) : 91.19961 98.15148 89.91161 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17340 grid for indexing accessible points = 1.400000 m= 22727 mr = 42248 m= 3706 mr = 17218 m= 195 mr = 2413 m= 0 mr = 63 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 657 time to turn everything in is 0.3300000 number of dielectric boundary points 25997 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14441 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) : 0.6554238 object centre at (A) : 15.01700 22.33950 3.672000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0177697E-02 1.3954399E-02 midg,1,midg; midg,igrid,midg 4.3676123E-02 -7.8981267E-03 1,midg,midg; igrid,midg,midg 7.9828501E-03 -6.1167278E-03 gauss-seidel spectral radius is 0.9986380 estimated iterations to convergence 215 setup time was (sec) 0.5900000 now iterating at: 14:11:49 rms-change max change #iterations 3.861539 168.4548 at 10iterations 1.818389 67.59798 at 20iterations 0.8522806 33.55713 at 30iterations 0.3980227 13.47248 at 40iterations 0.1871313 6.454460 at 50iterations 8.7618791E-02 3.042203 at 60iterations 4.0954817E-02 1.452492 at 70iterations 1.9155255E-02 0.6986437 at 80iterations 8.9868028E-03 0.3257618 at 90iterations 4.2059459E-03 0.1342327 at 100iterations 1.9728285E-03 6.9086075E-02 at 110iterations 9.2428667E-04 3.1559944E-02 at 120iterations finished qdiffx linear iterations at : 14:12:13 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 9.2428667E-04 3.1559944E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 14:12:14 8.792u 0.242s 0:30.86 29.2% 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 Tue Nov 22 2011 at 14:12:16 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 2.949407 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): -4.297000 34.33100 ymin,ymax (A): -3.440000 48.11900 zmin,zma (A): -23.48600 30.83000 x,y,z range (A): 38.62800 51.55900 54.31600 scale (grids/A): 2.949407 object centre (A): 15.01700 22.33950 3.672000 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 293.1439 centred at (gu) : 91.34576 101.6550 90.13550 assigned negative charge : -290.1442 centred at (gu) : 91.79940 102.2273 89.86749 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 141669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17340 grid for indexing accessible points = 1.400000 m= 72426 mr = 102446 m= 27664 mr = 59885 m= 6862 mr = 22803 m= 915 mr = 5302 m= 33 mr = 597 m= 0 mr = 7 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2192 time to turn everything in is 0.8400000 number of dielectric boundary points 58529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14624 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) : 1.966271 object centre at (A) : 15.01700 22.33950 3.672000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.082262 3.4085296E-02 midg,1,midg; midg,igrid,midg 0.4572033 -0.1531869 1,midg,midg; igrid,midg,midg 5.1486287E-02 -4.2526793E-02 gauss-seidel spectral radius is 0.9992478 estimated iterations to convergence 288 setup time was (sec) 1.100000 now iterating at: 14:12:23 rms-change max change #iterations 9.000825 404.6281 at 10iterations 5.182096 131.5760 at 20iterations 2.979854 63.91692 at 30iterations 1.708462 36.58823 at 40iterations 0.9823062 19.22855 at 50iterations 0.5606673 11.50678 at 60iterations 0.3210009 6.322250 at 70iterations 0.1830933 3.631664 at 80iterations 0.1046460 2.176559 at 90iterations 5.9902515E-02 1.151125 at 100iterations 3.4164887E-02 0.6611252 at 110iterations 1.9556873E-02 0.4381351 at 120iterations 1.1180489E-02 0.2251682 at 130iterations 6.3778283E-03 0.1172409 at 140iterations 3.6344370E-03 7.0001602E-02 at 150iterations 2.0810433E-03 4.8035622E-02 at 160iterations 1.1862939E-03 2.3612976E-02 at 170iterations 6.7820511E-04 1.4186859E-02 at 180iterations finished qdiffx linear iterations at : 14:13:02 total time elapsed so far: 14.11000 # loops : 180 mean,max change (kT/e) : 6.7820511E-04 1.4186859E-02 energy calculations done at 14.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.24000 DelPhi exited at 14:13:03 14.244u 0.272s 0:47.09 30.8% 0+0k 0+0io 0pf+0w