Sat Oct 8 11:38:15 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 8 2011 at 11:38:15 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2548 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5749354 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): -10.48000 37.23600 ymin,ymax (A): -34.30800 27.61200 zmin,zma (A): -13.97400 39.46300 x,y,z range (A): 47.71600 61.92000 53.43700 scale (grids/A): 0.5749354 object centre (A): 13.37800 -3.348001 12.74450 number of atom coordinates read : 2548 total number of charged atoms : 2398 net assigned charge : -2.999990 assigned positive charge : 372.4138 centred at (gu) : 90.15575 90.79762 91.59679 assigned negative charge : -375.4143 centred at (gu) : 90.12170 90.86143 91.51516 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5510 nv = 96 ne = 84 npr = 51424 no. pairs analyzed = 51424 no. exposed pairs = 3387 no. arc points = 23849 no. surface atoms = 1147 nbur = 1401 mkacc time = 0.1300000 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 = 1.484000 m= 231 mr = 2745 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2345 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 7027 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2723578E-09 1.0520343E-09 midg,1,midg; midg,igrid,midg 3.5109476E-10 -1.8938182E-09 1,midg,midg; igrid,midg,midg -1.0566099E-09 -3.0424580E-11 gauss-seidel spectral radius is 0.9843572 estimated iterations to convergence 66 setup time was (sec) 0.8500000 now iterating at: 11:38:16 rms-change max change #iterations 8.9495592E-02 15.71463 at 10iterations 6.7822356E-03 1.122360 at 20iterations 5.1486428E-04 7.9574585E-02 at 30iterations 4.1114199E-05 5.7678223E-03 at 40iterations 3.4891257E-06 6.1035156E-04 at 50iterations finished qdiffx linear iterations at : 11:38:22 total time elapsed so far: 6.940000 # loops : 50 mean,max change (kT/e) : 3.4891257E-06 6.1035156E-04 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 11:38:23 7.138u 0.720s 0:08.20 95.7% 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 8 2011 at 11:38:23 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2548 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.724806 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): -10.48000 37.23600 ymin,ymax (A): -34.30800 27.61200 zmin,zma (A): -13.97400 39.46300 x,y,z range (A): 47.71600 61.92000 53.43700 scale (grids/A): 1.724806 object centre (A): 13.37800 -3.348001 12.74450 number of atom coordinates read : 2548 total number of charged atoms : 2398 net assigned charge : -2.999990 assigned positive charge : 372.4138 centred at (gu) : 90.46651 92.39216 94.78961 assigned negative charge : -375.4143 centred at (gu) : 90.36486 92.58390 94.54534 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23849 grid for indexing accessible points = 1.400000 m= 18658 mr = 40068 m= 2023 mr = 12717 m= 83 mr = 1031 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 156 time to turn everything in is 0.6500000 number of dielectric boundary points 27692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 18575 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) : 0.5749354 object centre at (A) : 13.37800 -3.348001 12.74450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1605316E-02 8.0669904E-03 midg,1,midg; midg,igrid,midg 7.4599235E-04 -2.1929543E-02 1,midg,midg; igrid,midg,midg -8.2119359E-03 3.2900902E-03 gauss-seidel spectral radius is 0.9983369 estimated iterations to convergence 195 setup time was (sec) 1.190000 now iterating at: 11:38:25 rms-change max change #iterations 3.417219 186.4621 at 10iterations 1.474293 63.69376 at 20iterations 0.6358661 22.19590 at 30iterations 0.2751949 10.99965 at 40iterations 0.1186584 4.298126 at 50iterations 5.1283345E-02 1.852279 at 60iterations 2.2140613E-02 0.7944384 at 70iterations 9.5986184E-03 0.3176346 at 80iterations 4.1579818E-03 0.1695552 at 90iterations 1.7994185E-03 7.0705891E-02 at 100iterations 7.8139745E-04 2.7596474E-02 at 110iterations 3.3841759E-04 1.2029648E-02 at 120iterations finished qdiffx linear iterations at : 11:38:42 total time elapsed so far: 18.59000 # loops : 120 mean,max change (kT/e) : 3.3841759E-04 1.2029648E-02 energy calculations done at 18.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.78000 DelPhi exited at 11:38:43 18.788u 0.813s 0:19.91 98.3% 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 8 2011 at 11:38:43 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2548 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.587209 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): -10.48000 37.23600 ymin,ymax (A): -34.30800 27.61200 zmin,zma (A): -13.97400 39.46300 x,y,z range (A): 47.71600 61.92000 53.43700 scale (grids/A): 2.587209 object centre (A): 13.37800 -3.348001 12.74450 number of atom coordinates read : 2548 total number of charged atoms : 2398 net assigned charge : -2.999990 assigned positive charge : 372.4138 centred at (gu) : 90.69960 93.58794 97.18431 assigned negative charge : -375.4143 centred at (gu) : 90.54726 93.87582 96.81801 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 140981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23849 grid for indexing accessible points = 1.400000 m= 63758 mr = 98163 m= 18757 mr = 49972 m= 3267 mr = 14061 m= 235 mr = 2159 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 571 time to turn everything in is 1.440000 number of dielectric boundary points 62554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 19172 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) : 1.724806 object centre at (A) : 13.37800 -3.348001 12.74450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1612574 0.1763719 midg,1,midg; midg,igrid,midg 9.4079070E-02 -0.6236903 1,midg,midg; igrid,midg,midg -0.1194822 6.7353308E-02 gauss-seidel spectral radius is 0.9991747 estimated iterations to convergence 275 setup time was (sec) 1.850000 now iterating at: 11:38:45 rms-change max change #iterations 8.614952 358.3720 at 10iterations 4.900668 149.7859 at 20iterations 2.771696 65.47993 at 30iterations 1.559702 35.16405 at 40iterations 0.8785516 19.46412 at 50iterations 0.4918403 11.11006 at 60iterations 0.2755193 6.756065 at 70iterations 0.1541900 4.154705 at 80iterations 8.6174615E-02 1.803612 at 90iterations 4.8057765E-02 1.087509 at 100iterations 2.6703827E-02 0.6973009 at 110iterations 1.4916159E-02 0.3020401 at 120iterations 8.3106048E-03 0.2044754 at 130iterations 4.6363999E-03 9.5092773E-02 at 140iterations 2.5866029E-03 5.6842804E-02 at 150iterations 1.4430481E-03 3.1875610E-02 at 160iterations 8.0669479E-04 1.9329309E-02 at 170iterations 4.5206287E-04 9.0899467E-03 at 180iterations finished qdiffx linear iterations at : 11:39:15 total time elapsed so far: 30.91000 # loops : 180 mean,max change (kT/e) : 4.5206287E-04 9.0899467E-03 energy calculations done at 30.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.08000 DelPhi exited at 11:39:15 31.087u 0.793s 0:32.18 99.0% 0+0k 0+0io 0pf+0w