Mon Oct 10 01:18:27 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 Mon Oct 10 2011 at 01:18:27 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 0.6449742 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): -34.67000 10.64300 ymin,ymax (A): 1.399000 41.71500 zmin,zma (A): -0.2900000 54.90600 x,y,z range (A): 45.31300 40.31600 55.19600 scale (grids/A): 0.6449742 object centre (A): -12.01350 21.55700 27.30800 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 289.8650 centred at (gu) : 90.12286 89.26681 90.41578 assigned negative charge : -286.8653 centred at (gu) : 90.05024 89.39421 90.39854 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5509 nv = 96 ne = 84 npr = 40727 no. pairs analyzed = 40727 no. exposed pairs = 2428 no. arc points = 16786 no. surface atoms = 824 nbur = 1138 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 267 mr = 3084 m= 2 mr = 31 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 0.2500000 number of dielectric boundary points 2663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1675 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6448 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9638740E-09 7.2170825E-09 midg,1,midg; midg,igrid,midg 2.0262179E-08 -6.6378210E-09 1,midg,midg; igrid,midg,midg -2.2305247E-09 1.2345564E-08 gauss-seidel spectral radius is 0.9874858 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 01:18:28 rms-change max change #iterations 0.1323411 21.76219 at 10iterations 1.3154828E-02 1.896042 at 20iterations 1.2980722E-03 0.1918859 at 30iterations 1.3044715E-04 2.0731926E-02 at 40iterations 1.3277961E-05 1.9912720E-03 at 50iterations finished qdiffx linear iterations at : 01:18:31 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 1.3277961E-05 1.9912720E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 01:18:32 4.270u 0.284s 0:04.84 94.0% 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 Mon Oct 10 2011 at 01:18:32 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 1.934923 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): -34.67000 10.64300 ymin,ymax (A): 1.399000 41.71500 zmin,zma (A): -0.2900000 54.90600 x,y,z range (A): 45.31300 40.31600 55.19600 scale (grids/A): 1.934923 object centre (A): -12.01350 21.55700 27.30800 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 289.8650 centred at (gu) : 90.36866 87.80055 91.24747 assigned negative charge : -286.8653 centred at (gu) : 90.15080 88.18266 91.19576 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16786 grid for indexing accessible points = 1.400000 m= 22493 mr = 40629 m= 3738 mr = 17309 m= 204 mr = 2460 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 24763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 14338 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) : 0.6449742 object centre at (A) : -12.01350 21.55700 27.30800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2076552E-02 5.3032767E-02 midg,1,midg; midg,igrid,midg 6.9167577E-03 -1.0465563E-02 1,midg,midg; igrid,midg,midg -2.5419060E-03 -4.3398933E-03 gauss-seidel spectral radius is 0.9985993 estimated iterations to convergence 212 setup time was (sec) 0.8200000 now iterating at: 01:18:33 rms-change max change #iterations 3.722128 171.2039 at 10iterations 1.728900 62.51035 at 20iterations 0.8050773 29.63491 at 30iterations 0.3730654 13.47647 at 40iterations 0.1732758 6.087334 at 50iterations 8.0066763E-02 2.816078 at 60iterations 3.7017081E-02 1.325445 at 70iterations 1.7223680E-02 0.6226130 at 80iterations 7.9766922E-03 0.2678368 at 90iterations 3.7022545E-03 0.1323407 at 100iterations 1.7198254E-03 6.3194275E-02 at 110iterations 7.9606014E-04 2.7707577E-02 at 120iterations finished qdiffx linear iterations at : 01:18:41 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 7.9606014E-04 2.7707577E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 01:18:42 9.701u 0.317s 0:10.34 96.8% 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 Mon Oct 10 2011 at 01:18:42 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 2.902384 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): -34.67000 10.64300 ymin,ymax (A): 1.399000 41.71500 zmin,zma (A): -0.2900000 54.90600 x,y,z range (A): 45.31300 40.31600 55.19600 scale (grids/A): 2.902384 object centre (A): -12.01350 21.55700 27.30800 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 289.8650 centred at (gu) : 90.55299 86.70077 91.87125 assigned negative charge : -286.8653 centred at (gu) : 90.22628 87.27412 91.79382 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 135582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16786 grid for indexing accessible points = 1.400000 m= 71179 mr = 97981 m= 27825 mr = 59386 m= 6838 mr = 23268 m= 864 mr = 5301 m= 50 mr = 539 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.7099999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 55834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 14552 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) : 1.934923 object centre at (A) : -12.01350 21.55700 27.30800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6487320E-02 0.4093657 midg,1,midg; midg,igrid,midg 1.4691572E-02 -0.1272490 1,midg,midg; igrid,midg,midg -7.2495222E-02 -8.0274500E-02 gauss-seidel spectral radius is 0.9992326 estimated iterations to convergence 285 setup time was (sec) 1.700000 now iterating at: 01:18:44 rms-change max change #iterations 8.701768 364.3302 at 10iterations 4.998959 120.0458 at 20iterations 2.850205 58.50383 at 30iterations 1.628280 40.25978 at 40iterations 0.9276816 17.92408 at 50iterations 0.5266989 10.23383 at 60iterations 0.2994531 5.765251 at 70iterations 0.1705073 3.312289 at 80iterations 9.6641369E-02 2.039190 at 90iterations 5.4998901E-02 1.126367 at 100iterations 3.1235274E-02 0.6313972 at 110iterations 1.7725525E-02 0.3708773 at 120iterations 1.0051915E-02 0.1818547 at 130iterations 5.7197339E-03 0.1137829 at 140iterations 3.2485360E-03 6.1538696E-02 at 150iterations 1.8427876E-03 3.8656235E-02 at 160iterations 1.0491726E-03 2.1324158E-02 at 170iterations 5.9869536E-04 1.2038231E-02 at 180iterations finished qdiffx linear iterations at : 01:18:58 total time elapsed so far: 15.48000 # loops : 180 mean,max change (kT/e) : 5.9869536E-04 1.2038231E-02 energy calculations done at 15.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.66000 DelPhi exited at 01:18:58 15.666u 0.299s 0:16.24 98.2% 0+0k 0+0io 0pf+0w