Sat Oct 8 15:52:32 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 8 2011 at 15:52:32 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 = 2350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6219535 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 0.6219535 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2350 total number of charged atoms : 2255 net assigned charge : 3.000001 assigned positive charge : 345.8231 centred at (gu) : 90.19542 88.35288 89.61085 assigned negative charge : -342.8238 centred at (gu) : 90.22377 88.45016 89.66176 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6080 nv = 96 ne = 84 npr = 47760 no. pairs analyzed = 47760 no. exposed pairs = 2885 no. arc points = 19999 no. surface atoms = 988 nbur = 1362 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3355 m= 0 mr = 36 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 2981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0719247E-09 -6.6329170E-10 midg,1,midg; midg,igrid,midg 1.2122825E-08 -2.5032147E-09 1,midg,midg; igrid,midg,midg 4.0164694E-09 6.9946793E-10 gauss-seidel spectral radius is 0.9865904 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 15:52:33 rms-change max change #iterations 0.1184718 18.04797 at 10iterations 1.1155257E-02 2.078049 at 20iterations 1.0856475E-03 0.1626740 at 30iterations 1.2853746E-04 2.5148392E-02 at 40iterations 2.4562527E-05 4.9610138E-03 at 50iterations finished qdiffx linear iterations at : 15:52:36 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 2.4562527E-05 4.9610138E-03 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 15:52:37 4.348u 0.244s 0:04.90 93.4% 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 Sat Oct 8 2011 at 15:52:37 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 = 2350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.865861 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 1.865861 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2350 total number of charged atoms : 2255 net assigned charge : 3.000001 assigned positive charge : 345.8231 centred at (gu) : 90.58569 85.05785 88.83218 assigned negative charge : -342.8238 centred at (gu) : 90.67140 85.35017 88.98531 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66002 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19999 grid for indexing accessible points = 1.400000 m= 22814 mr = 46034 m= 3481 mr = 16720 m= 181 mr = 2219 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 332 time to turn everything in is 0.5200000 number of dielectric boundary points 27437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17702 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) : 0.6219535 object centre at (A) : 21.54850 7.176000 10.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0882800E-02 -4.8379148E-03 midg,1,midg; midg,igrid,midg 2.0442801E-02 -1.8462014E-03 1,midg,midg; igrid,midg,midg 3.2327673E-03 -2.9854421E-02 gauss-seidel spectral radius is 0.9985506 estimated iterations to convergence 208 setup time was (sec) 0.8400000 now iterating at: 15:52:38 rms-change max change #iterations 3.812720 183.7491 at 10iterations 1.737067 72.52017 at 20iterations 0.7958111 27.17022 at 30iterations 0.3650409 12.34112 at 40iterations 0.1666815 6.204627 at 50iterations 7.6511838E-02 2.647431 at 60iterations 3.4954712E-02 1.177244 at 70iterations 1.6035244E-02 0.5420609 at 80iterations 7.3498623E-03 0.2515659 at 90iterations 3.3791487E-03 0.1104012 at 100iterations 1.5509215E-03 5.3436756E-02 at 110iterations 7.1506907E-04 2.4756432E-02 at 120iterations finished qdiffx linear iterations at : 15:52:46 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 7.1506907E-04 2.4756432E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 15:52:47 9.614u 0.264s 0:10.23 96.4% 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 Sat Oct 8 2011 at 15:52:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2350 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: 2.798791 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 2.798791 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2350 total number of charged atoms : 2255 net assigned charge : 3.000001 assigned positive charge : 345.8231 centred at (gu) : 90.87838 82.58682 88.24825 assigned negative charge : -342.8238 centred at (gu) : 91.00710 83.02515 88.47796 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 152721 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19999 grid for indexing accessible points = 1.400000 m= 74655 mr = 111627 m= 26409 mr = 60958 m= 6405 mr = 21189 m= 809 mr = 4956 m= 45 mr = 522 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 1072 time to turn everything in is 1.410000 number of dielectric boundary points 61772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 18034 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) : 1.865861 object centre at (A) : 21.54850 7.176000 10.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2125274 -0.1455010 midg,1,midg; midg,igrid,midg 0.1721262 -4.6334144E-02 1,midg,midg; igrid,midg,midg 2.8958138E-02 -0.4619132 gauss-seidel spectral radius is 0.9992284 estimated iterations to convergence 284 setup time was (sec) 1.770000 now iterating at: 15:52:49 rms-change max change #iterations 9.069725 345.7045 at 10iterations 5.259114 125.8453 at 20iterations 3.020409 62.33163 at 30iterations 1.736094 34.11655 at 40iterations 0.9929826 19.47412 at 50iterations 0.5679923 12.11359 at 60iterations 0.3242016 6.338999 at 70iterations 0.1848177 3.793480 at 80iterations 0.1054044 1.935447 at 90iterations 6.0005330E-02 1.151581 at 100iterations 3.4142870E-02 0.6097717 at 110iterations 1.9416861E-02 0.3730927 at 120iterations 1.1065985E-02 0.2363091 at 130iterations 6.3007316E-03 0.1252084 at 140iterations 3.5935270E-03 6.9793701E-02 at 150iterations 2.0594709E-03 4.3697357E-02 at 160iterations 1.1845176E-03 2.3320198E-02 at 170iterations 6.8706629E-04 1.3852596E-02 at 180iterations finished qdiffx linear iterations at : 15:53:03 total time elapsed so far: 15.23000 # loops : 180 mean,max change (kT/e) : 6.8706629E-04 1.3852596E-02 energy calculations done at 15.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.42000 DelPhi exited at 15:53:03 15.421u 0.281s 0:15.97 98.3% 0+0k 0+0io 0pf+0w