Sun Oct 9 12:27:07 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 Sun Oct 9 2011 at 12:27:08 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 = 2400 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: 0.6801421 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): -5.662000 43.96100 ymin,ymax (A): -14.08900 38.25300 zmin,zma (A): 2.067000 45.23900 x,y,z range (A): 49.62300 52.34200 43.17200 scale (grids/A): 0.6801421 object centre (A): 19.14950 12.08200 23.65300 number of atom coordinates read : 2400 total number of charged atoms : 2257 net assigned charge : 2.500024 assigned positive charge : 365.8480 centred at (gu) : 89.33475 90.78090 90.51850 assigned negative charge : -363.3484 centred at (gu) : 89.34429 90.98267 90.59122 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7375 nv = 96 ne = 84 npr = 48408 no. pairs analyzed = 48408 no. exposed pairs = 2967 no. arc points = 20665 no. surface atoms = 997 nbur = 1403 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 4083 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.1700000 number of dielectric boundary points 3647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2028 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0193121E-08 -1.2170109E-08 midg,1,midg; midg,igrid,midg 6.1255896E-08 -6.0581961E-08 1,midg,midg; igrid,midg,midg 1.6451354E-08 7.5610069E-09 gauss-seidel spectral radius is 0.9887704 estimated iterations to convergence 77 setup time was (sec) 0.3500000 now iterating at: 12:27:08 rms-change max change #iterations 0.1798373 31.60736 at 10iterations 2.0789519E-02 2.746117 at 20iterations 2.7290867E-03 0.3737640 at 30iterations 5.2881578E-04 8.3305359E-02 at 40iterations 1.4734478E-04 2.3563385E-02 at 50iterations finished qdiffx linear iterations at : 12:27:11 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.4734478E-04 2.3563385E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 12:27:11 3.318u 0.194s 0:03.79 92.3% 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 Sun Oct 9 2011 at 12:27:11 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 = 2400 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: 2.040426 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): -5.662000 43.96100 ymin,ymax (A): -14.08900 38.25300 zmin,zma (A): 2.067000 45.23900 x,y,z range (A): 49.62300 52.34200 43.17200 scale (grids/A): 2.040426 object centre (A): 19.14950 12.08200 23.65300 number of atom coordinates read : 2400 total number of charged atoms : 2257 net assigned charge : 2.500024 assigned positive charge : 365.8480 centred at (gu) : 88.00353 92.34197 91.55511 assigned negative charge : -363.3484 centred at (gu) : 88.03248 92.94778 91.77340 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 29328 mr = 55607 m= 4913 mr = 21509 m= 419 mr = 3146 m= 9 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 254 time to turn everything in is 0.3800000 number of dielectric boundary points 33570 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17877 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) : 0.6801421 object centre at (A) : 19.14950 12.08200 23.65300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3624390E-02 5.3096619E-03 midg,1,midg; midg,igrid,midg 2.3416113E-02 -8.7422766E-02 1,midg,midg; igrid,midg,midg 4.4668581E-02 -1.0758862E-02 gauss-seidel spectral radius is 0.9987829 estimated iterations to convergence 227 setup time was (sec) 0.6000000 now iterating at: 12:27:12 rms-change max change #iterations 4.665399 193.6058 at 10iterations 2.270146 78.06020 at 20iterations 1.106042 36.96898 at 30iterations 0.5413331 15.59950 at 40iterations 0.2640547 8.750021 at 50iterations 0.1289765 3.804040 at 60iterations 6.3355207E-02 1.930058 at 70iterations 3.1049009E-02 0.9039490 at 80iterations 1.5261977E-02 0.4403377 at 90iterations 7.5774337E-03 0.2481918 at 100iterations 3.7923858E-03 0.1243801 at 110iterations 1.9541080E-03 5.5985451E-02 at 120iterations finished qdiffx linear iterations at : 12:27:19 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.9541080E-03 5.5985451E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 12:27:20 7.725u 0.187s 0:08.26 95.6% 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 Sun Oct 9 2011 at 12:27:20 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 = 2400 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: 3.060639 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): -5.662000 43.96100 ymin,ymax (A): -14.08900 38.25300 zmin,zma (A): 2.067000 45.23900 x,y,z range (A): 49.62300 52.34200 43.17200 scale (grids/A): 3.060639 object centre (A): 19.14950 12.08200 23.65300 number of atom coordinates read : 2400 total number of charged atoms : 2257 net assigned charge : 2.500024 assigned positive charge : 365.8480 centred at (gu) : 87.00516 93.51298 92.33252 assigned negative charge : -363.3484 centred at (gu) : 87.04868 94.42159 92.66012 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 182956 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 94697 mr = 134033 m= 34819 mr = 77626 m= 9001 mr = 27930 m= 1701 mr = 6786 m= 189 mr = 1247 m= 1 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 923 time to turn everything in is 1.010000 number of dielectric boundary points 75633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 18056 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) : 2.040426 object centre at (A) : 19.14950 12.08200 23.65300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4080942 -1.9725038E-02 midg,1,midg; midg,igrid,midg 0.5147256 -0.9954041 1,midg,midg; igrid,midg,midg 0.4934659 -0.2924948 gauss-seidel spectral radius is 0.9992873 estimated iterations to convergence 296 setup time was (sec) 1.250000 now iterating at: 12:27:21 rms-change max change #iterations 10.66478 434.3758 at 10iterations 6.299836 137.8028 at 20iterations 3.722579 74.98145 at 30iterations 2.187259 49.67194 at 40iterations 1.283466 26.08569 at 50iterations 0.7507543 16.26000 at 60iterations 0.4396951 7.897028 at 70iterations 0.2579399 5.112557 at 80iterations 0.1505006 2.881762 at 90iterations 8.7801039E-02 1.565574 at 100iterations 5.1392883E-02 0.8674984 at 110iterations 3.0136330E-02 0.5388947 at 120iterations 1.7764682E-02 0.2903442 at 130iterations 1.0624243E-02 0.1957016 at 140iterations 6.4703370E-03 0.1239929 at 150iterations 4.0686140E-03 8.2216263E-02 at 160iterations 2.6903255E-03 6.3301086E-02 at 170iterations 1.8850357E-03 4.1179657E-02 at 180iterations finished qdiffx linear iterations at : 12:27:32 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 1.8850357E-03 4.1179657E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 12:27:33 12.610u 0.197s 0:13.08 97.8% 0+0k 0+0io 0pf+0w