Tue Nov 8 08:33:23 PST 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 Nov 8 2011 at 08:33:23 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 ! Automatically converted by prot2crg.py # of charge parameter records: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 0.6331590 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): -28.02200 21.85300 ymin,ymax (A): -24.85600 24.13500 zmin,zma (A): -23.95600 32.27000 x,y,z range (A): 49.87500 48.99100 56.22600 scale (grids/A): 0.6331590 object centre (A): -3.084499 -0.3605003 4.157001 number of atom coordinates read : 2393 total number of charged atoms : 2248 net assigned charge : 7.5399876E-06 assigned positive charge : 351.7182 centred at (gu) : 91.63332 91.32357 88.61794 assigned negative charge : -351.7189 centred at (gu) : 91.65425 91.20290 88.77842 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6541 nv = 96 ne = 84 npr = 48215 no. pairs analyzed = 48215 no. exposed pairs = 3072 no. arc points = 22246 no. surface atoms = 1031 nbur = 1362 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3466 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.2200000 number of dielectric boundary points 3405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2239 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7844 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8214454E-08 -1.0743515E-08 midg,1,midg; midg,igrid,midg -8.2058911E-09 1.3471847E-08 1,midg,midg; igrid,midg,midg 1.0482607E-09 -3.0877609E-09 gauss-seidel spectral radius is 0.9870664 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 08:33:24 rms-change max change #iterations 0.1298952 21.74629 at 10iterations 1.2580629E-02 2.048320 at 20iterations 1.2064109E-03 0.1930275 at 30iterations 1.1523018E-04 1.5602112E-02 at 40iterations 1.1046865E-05 1.9860268E-03 at 50iterations finished qdiffx linear iterations at : 08:33:27 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.1046865E-05 1.9860268E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 08:33:27 3.511u 0.178s 0:04.12 89.3% 0+0k 0+45752io 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 Nov 8 2011 at 08:33:28 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 ! Automatically converted by prot2crg.py # of charge parameter records: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 1.899477 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): -28.02200 21.85300 ymin,ymax (A): -24.85600 24.13500 zmin,zma (A): -23.95600 32.27000 x,y,z range (A): 49.87500 48.99100 56.22600 scale (grids/A): 1.899477 object centre (A): -3.084499 -0.3605003 4.157001 number of atom coordinates read : 2393 total number of charged atoms : 2248 net assigned charge : 7.5399876E-06 assigned positive charge : 351.7182 centred at (gu) : 94.89947 93.97029 85.85341 assigned negative charge : -351.7189 centred at (gu) : 94.96266 93.60883 86.33530 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70300 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22246 grid for indexing accessible points = 1.400000 m= 25247 mr = 47566 m= 3852 mr = 18254 m= 201 mr = 2285 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 631 time to turn everything in is 0.4400000 number of dielectric boundary points 31452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17671 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) : 0.6331590 object centre at (A) : -3.084499 -0.3605003 4.157001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8556118E-02 -6.2264096E-02 midg,1,midg; midg,igrid,midg -1.1689176E-02 7.7041667E-03 1,midg,midg; igrid,midg,midg 8.5278358E-03 -1.3756156E-03 gauss-seidel spectral radius is 0.9986085 estimated iterations to convergence 212 setup time was (sec) 0.6600000 now iterating at: 08:33:28 rms-change max change #iterations 3.973703 172.1621 at 10iterations 1.843999 66.79401 at 20iterations 0.8557570 28.60454 at 30iterations 0.3989372 15.24147 at 40iterations 0.1840934 6.415644 at 50iterations 8.5968889E-02 2.827433 at 60iterations 3.9828230E-02 1.297038 at 70iterations 1.8522061E-02 0.6380496 at 80iterations 8.6364979E-03 0.3052239 at 90iterations 4.0042009E-03 0.1415186 at 100iterations 1.8556011E-03 5.9524536E-02 at 110iterations 8.6378155E-04 3.2150269E-02 at 120iterations finished qdiffx linear iterations at : 08:33:36 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 8.6378155E-04 3.2150269E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 08:33:36 8.020u 0.193s 0:08.57 95.7% 0+0k 0+45216io 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 Nov 8 2011 at 08:33:36 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 ! Automatically converted by prot2crg.py # of charge parameter records: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 2.849216 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): -28.02200 21.85300 ymin,ymax (A): -24.85600 24.13500 zmin,zma (A): -23.95600 32.27000 x,y,z range (A): 49.87500 48.99100 56.22600 scale (grids/A): 2.849216 object centre (A): -3.084499 -0.3605003 4.157001 number of atom coordinates read : 2393 total number of charged atoms : 2248 net assigned charge : 7.5399876E-06 assigned positive charge : 351.7182 centred at (gu) : 97.34908 95.95517 83.78001 assigned negative charge : -351.7189 centred at (gu) : 97.44394 95.41316 84.50285 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22246 grid for indexing accessible points = 1.400000 m= 80467 mr = 114866 m= 29648 mr = 65131 m= 6877 mr = 23444 m= 827 mr = 4994 m= 37 mr = 473 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 2331 time to turn everything in is 1.140000 number of dielectric boundary points 71055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 17983 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) : 1.899477 object centre at (A) : -3.084499 -0.3605003 4.157001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2676071 -0.7528281 midg,1,midg; midg,igrid,midg -0.1017466 5.2091520E-02 1,midg,midg; igrid,midg,midg 9.4220370E-02 -3.1206314E-02 gauss-seidel spectral radius is 0.9992545 estimated iterations to convergence 289 setup time was (sec) 1.370000 now iterating at: 08:33:38 rms-change max change #iterations 9.413764 361.3254 at 10iterations 5.466404 128.0538 at 20iterations 3.160361 91.73051 at 30iterations 1.824459 38.46292 at 40iterations 1.050452 22.20818 at 50iterations 0.6049528 12.84079 at 60iterations 0.3478805 6.907097 at 70iterations 0.1996929 4.040833 at 80iterations 0.1145755 2.180262 at 90iterations 6.5716818E-02 1.289726 at 100iterations 3.7752721E-02 0.8020020 at 110iterations 2.1617608E-02 0.3765182 at 120iterations 1.2356105E-02 0.2296178 at 130iterations 7.0784669E-03 0.1500604 at 140iterations 4.0679276E-03 7.1380615E-02 at 150iterations 2.3310040E-03 4.7790527E-02 at 160iterations 1.3330589E-03 2.6432037E-02 at 170iterations 7.6527067E-04 1.3790131E-02 at 180iterations finished qdiffx linear iterations at : 08:33:49 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 7.6527067E-04 1.3790131E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 08:33:50 12.948u 0.215s 0:13.49 97.4% 0+0k 0+45208io 0pf+0w