Tue Oct 11 06:10:06 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 06:10:06 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7157937 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): 2.629000 47.58400 ymin,ymax (A): 1.871000 40.71700 zmin,zma (A): -2.759000 46.97600 x,y,z range (A): 44.95500 38.84600 49.73500 scale (grids/A): 0.7157937 object centre (A): 25.10650 21.29400 22.10850 number of atom coordinates read : 2209 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.18724 90.31954 90.53544 assigned negative charge : -305.3172 centred at (gu) : 90.36868 90.30898 90.56179 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7086 nv = 96 ne = 84 npr = 39759 no. pairs analyzed = 39759 no. exposed pairs = 2437 no. arc points = 16994 no. surface atoms = 834 nbur = 1375 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4046 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1632 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3771866E-08 6.8340235E-08 midg,1,midg; midg,igrid,midg 6.7087676E-08 8.8596657E-08 1,midg,midg; igrid,midg,midg 1.7459283E-07 -3.1473309E-08 gauss-seidel spectral radius is 0.9898188 estimated iterations to convergence 81 setup time was (sec) 0.5100000 now iterating at: 06:10:06 rms-change max change #iterations 0.2057823 29.99578 at 10iterations 2.6305234E-02 4.120159 at 20iterations 3.4360075E-03 0.4914579 at 30iterations 4.9480057E-04 6.6446304E-02 at 40iterations 1.0186021E-04 1.4820099E-02 at 50iterations finished qdiffx linear iterations at : 06:10:09 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.0186021E-04 1.4820099E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 06:10:10 3.544u 0.205s 0:04.20 89.0% 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 06:10:10 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.147381 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): 2.629000 47.58400 ymin,ymax (A): 1.871000 40.71700 zmin,zma (A): -2.759000 46.97600 x,y,z range (A): 44.95500 38.84600 49.73500 scale (grids/A): 2.147381 object centre (A): 25.10650 21.29400 22.10850 number of atom coordinates read : 2209 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.56158 90.95869 91.60609 assigned negative charge : -305.3172 centred at (gu) : 91.10604 90.92715 91.68531 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 75250 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16994 grid for indexing accessible points = 1.400000 m= 30396 mr = 53498 m= 5868 mr = 23164 m= 552 mr = 3859 m= 11 mr = 307 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15280 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) : 0.7157937 object centre at (A) : 25.10650 21.29400 22.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1741909E-02 6.7169391E-02 midg,1,midg; midg,igrid,midg 5.8877785E-03 3.3699349E-02 1,midg,midg; igrid,midg,midg 4.4281106E-02 7.5370041E-03 gauss-seidel spectral radius is 0.9988498 estimated iterations to convergence 233 setup time was (sec) 0.9300000 now iterating at: 06:10:11 rms-change max change #iterations 4.642793 179.5325 at 10iterations 2.304651 78.03085 at 20iterations 1.151012 36.07668 at 30iterations 0.5731712 17.48685 at 40iterations 0.2882078 8.909395 at 50iterations 0.1434415 4.156663 at 60iterations 7.1714073E-02 2.686867 at 70iterations 3.5820246E-02 1.071875 at 80iterations 1.7958334E-02 0.5189037 at 90iterations 9.0257730E-03 0.2864256 at 100iterations 4.5499285E-03 0.1303940 at 110iterations 2.3162304E-03 7.4729919E-02 at 120iterations finished qdiffx linear iterations at : 06:10:18 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 2.3162304E-03 7.4729919E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 06:10:19 8.317u 0.264s 0:08.98 95.4% 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 06:10:19 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.221072 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): 2.629000 47.58400 ymin,ymax (A): 1.871000 40.71700 zmin,zma (A): -2.759000 46.97600 x,y,z range (A): 44.95500 38.84600 49.73500 scale (grids/A): 3.221072 object centre (A): 25.10650 21.29400 22.10850 number of atom coordinates read : 2209 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.84241 91.43805 92.40913 assigned negative charge : -305.3172 centred at (gu) : 91.65903 91.39079 92.52817 start vw surface at 0.1500000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 173382 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16994 grid for indexing accessible points = 1.400000 m= 94817 mr = 128888 m= 38512 mr = 79081 m= 11125 mr = 31530 m= 2278 mr = 8614 m= 268 mr = 1649 m= 3 mr = 195 m= 0 mr = 2 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 70426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 15496 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) : 2.147381 object centre at (A) : 25.10650 21.29400 22.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4770484 0.6238583 midg,1,midg; midg,igrid,midg 1.6948232E-02 0.2607992 1,midg,midg; igrid,midg,midg 0.3442875 0.1281677 gauss-seidel spectral radius is 0.9992993 estimated iterations to convergence 298 setup time was (sec) 2.270000 now iterating at: 06:10:22 rms-change max change #iterations 10.36844 389.5370 at 10iterations 6.140158 149.6639 at 20iterations 3.636673 87.15762 at 30iterations 2.150372 50.20239 at 40iterations 1.266250 24.50467 at 50iterations 0.7439392 15.29389 at 60iterations 0.4386080 8.302237 at 70iterations 0.2583070 4.892743 at 80iterations 0.1512244 2.980916 at 90iterations 8.8921420E-02 1.546282 at 100iterations 5.2190714E-02 0.9580460 at 110iterations 3.0735571E-02 0.5778389 at 120iterations 1.8155817E-02 0.3269558 at 130iterations 1.0803401E-02 0.2070179 at 140iterations 6.5356689E-03 0.1259155 at 150iterations 4.0419670E-03 7.4249268E-02 at 160iterations 2.6188036E-03 5.1006317E-02 at 170iterations 1.7815856E-03 3.5732269E-02 at 180iterations finished qdiffx linear iterations at : 06:10:34 total time elapsed so far: 14.74000 # loops : 180 mean,max change (kT/e) : 1.7815856E-03 3.5732269E-02 energy calculations done at 14.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.95000 DelPhi exited at 06:10:35 14.947u 0.303s 0:15.76 96.7% 0+0k 0+0io 0pf+0w