Tue Oct 11 06:24:09 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 06:24:09 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 = 2057 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: 0.7213194 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): 3.377000 47.18100 ymin,ymax (A): 0.6380001 42.31600 zmin,zma (A): -2.605000 46.74900 x,y,z range (A): 43.80400 41.67800 49.35400 scale (grids/A): 0.7213194 object centre (A): 25.27900 21.47700 22.07200 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.88132 89.93620 90.38624 assigned negative charge : -304.2972 centred at (gu) : 90.06442 89.91328 90.42030 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7277 nv = 96 ne = 84 npr = 41608 no. pairs analyzed = 41608 no. exposed pairs = 2436 no. arc points = 16656 no. surface atoms = 831 nbur = 1226 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 4256 m= 6 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1554 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0198197E-07 6.9767793E-08 midg,1,midg; midg,igrid,midg 7.3234759E-08 1.0114294E-07 1,midg,midg; igrid,midg,midg 2.0967443E-07 -3.3547362E-08 gauss-seidel spectral radius is 0.9899747 estimated iterations to convergence 81 setup time was (sec) 0.5700000 now iterating at: 06:24:10 rms-change max change #iterations 0.2171083 31.08626 at 10iterations 2.8531063E-02 3.625569 at 20iterations 3.8583411E-03 0.4808301 at 30iterations 6.2280498E-04 9.2866898E-02 at 40iterations 1.4450712E-04 1.7370224E-02 at 50iterations finished qdiffx linear iterations at : 06:24:13 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.4450712E-04 1.7370224E-02 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 06:24:14 4.087u 0.281s 0:04.98 87.5% 0+0k 0+0io 6pf+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 06:24:14 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 = 2057 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: 2.163958 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): 3.377000 47.18100 ymin,ymax (A): 0.6380001 42.31600 zmin,zma (A): -2.605000 46.74900 x,y,z range (A): 43.80400 41.67800 49.35400 scale (grids/A): 2.163958 object centre (A): 25.27900 21.47700 22.07200 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.64409 89.80867 91.15865 assigned negative charge : -304.2972 centred at (gu) : 90.19347 89.73999 91.26093 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 77244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16656 grid for indexing accessible points = 1.400000 m= 31289 mr = 55495 m= 6429 mr = 24056 m= 589 mr = 4274 m= 14 mr = 294 m= 0 mr = 2 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 31444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 15333 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) : 0.7213194 object centre at (A) : 25.27900 21.47700 22.07200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3548476E-02 7.1673043E-02 midg,1,midg; midg,igrid,midg 5.4254448E-03 3.0969216E-02 1,midg,midg; igrid,midg,midg 5.0406653E-02 1.1710168E-02 gauss-seidel spectral radius is 0.9988664 estimated iterations to convergence 235 setup time was (sec) 1.010000 now iterating at: 06:24:15 rms-change max change #iterations 4.707735 186.3054 at 10iterations 2.347754 81.89304 at 20iterations 1.184538 36.86267 at 30iterations 0.5925990 19.10322 at 40iterations 0.2981794 8.205894 at 50iterations 0.1498799 4.609619 at 60iterations 7.5285457E-02 2.245747 at 70iterations 3.7698727E-02 1.085892 at 80iterations 1.8990826E-02 0.5553641 at 90iterations 9.6200733E-03 0.2761402 at 100iterations 4.8580947E-03 0.1403503 at 110iterations 2.4930220E-03 7.3022127E-02 at 120iterations finished qdiffx linear iterations at : 06:24:24 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 2.4930220E-03 7.3022127E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 06:24:25 9.664u 0.317s 0:10.82 92.1% 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 06:24:25 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 = 2057 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: 3.245938 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): 3.377000 47.18100 ymin,ymax (A): 0.6380001 42.31600 zmin,zma (A): -2.605000 46.74900 x,y,z range (A): 43.80400 41.67800 49.35400 scale (grids/A): 3.245938 object centre (A): 25.27900 21.47700 22.07200 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.46613 89.71309 91.73792 assigned negative charge : -304.2972 centred at (gu) : 90.29034 89.61012 91.89157 start vw surface at 0.1600000 fill in re-entrant regions at 1.030000 boundary points on vw surface= 178247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16656 grid for indexing accessible points = 1.400000 m= 97584 mr = 133528 m= 40151 mr = 81769 m= 12133 mr = 33316 m= 2498 mr = 9470 m= 293 mr = 1762 m= 12 mr = 199 m= 0 mr = 2 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.310000 number of dielectric boundary points 70872 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.450000 number of grid points assigned charge 15432 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) : 2.163958 object centre at (A) : 25.27900 21.47700 22.07200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5305079 0.6394877 midg,1,midg; midg,igrid,midg -1.3390946E-02 0.2206080 1,midg,midg; igrid,midg,midg 0.3550281 0.2102888 gauss-seidel spectral radius is 0.9993007 estimated iterations to convergence 298 setup time was (sec) 2.630000 now iterating at: 06:24:28 rms-change max change #iterations 10.39214 434.4826 at 10iterations 6.186316 138.8719 at 20iterations 3.658094 66.02727 at 30iterations 2.161351 39.35426 at 40iterations 1.275485 23.58558 at 50iterations 0.7513158 13.78504 at 60iterations 0.4433074 8.432733 at 70iterations 0.2609272 5.513601 at 80iterations 0.1530004 2.731504 at 90iterations 9.0107515E-02 1.586984 at 100iterations 5.3084251E-02 0.8994217 at 110iterations 3.1353477E-02 0.5150909 at 120iterations 1.8702786E-02 0.3314781 at 130iterations 1.1332000E-02 0.2001266 at 140iterations 7.0388461E-03 0.1280727 at 150iterations 4.5657260E-03 8.2813263E-02 at 160iterations 3.1283235E-03 5.8010101E-02 at 170iterations 2.2777757E-03 3.9155006E-02 at 180iterations finished qdiffx linear iterations at : 06:24:42 total time elapsed so far: 16.62000 # loops : 180 mean,max change (kT/e) : 2.2777757E-03 3.9155006E-02 energy calculations done at 16.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.81000 DelPhi exited at 06:24:42 16.807u 0.327s 0:17.42 98.2% 0+0k 0+0io 0pf+0w