Sat Oct 8 11:38:42 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 11:38:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4256 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5258028 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): -1.757000 65.94900 ymin,ymax (A): -10.24800 37.84100 zmin,zma (A): -19.70200 43.98100 x,y,z range (A): 67.70599 48.08900 63.68300 scale (grids/A): 0.5258028 object centre (A): 32.09600 13.79650 12.13950 number of atom coordinates read : 4256 total number of charged atoms : 4101 net assigned charge : -7.499957 assigned positive charge : 639.4351 centred at (gu) : 87.76511 89.82288 90.45221 assigned negative charge : -646.9375 centred at (gu) : 87.82343 89.90521 90.48990 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6734 nv = 96 ne = 84 npr = 95107 no. pairs analyzed = 95107 no. exposed pairs = 4414 no. arc points = 30255 no. surface atoms = 1511 nbur = 2745 mkacc time = 0.2400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 240 mr = 3774 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.4500000 number of dielectric boundary points 3189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3071 ## 428 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1774580E-11 -4.2289194E-10 midg,1,midg; midg,igrid,midg 1.5442111E-10 -5.5036087E-10 1,midg,midg; igrid,midg,midg 8.8236848E-11 -2.6670485E-10 gauss-seidel spectral radius is 0.9814347 estimated iterations to convergence 61 setup time was (sec) 0.7700000 now iterating at: 11:38:43 rms-change max change #iterations 7.1250468E-02 9.541510 at 10iterations 4.5999223E-03 0.7823820 at 20iterations 3.6953326E-04 6.4470291E-02 at 30iterations 5.2697342E-05 8.9073181E-03 at 40iterations 9.8037781E-06 1.6975403E-03 at 50iterations finished qdiffx linear iterations at : 11:38:48 total time elapsed so far: 4.850000 # loops : 50 mean,max change (kT/e) : 9.8037781E-06 1.6975403E-03 energy calculations done at 4.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.020000 DelPhi exited at 11:38:48 5.023u 0.390s 0:05.79 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 11:38:48 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 = 4256 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.577408 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): -1.757000 65.94900 ymin,ymax (A): -10.24800 37.84100 zmin,zma (A): -19.70200 43.98100 x,y,z range (A): 67.70599 48.08900 63.68300 scale (grids/A): 1.577408 object centre (A): 32.09600 13.79650 12.13950 number of atom coordinates read : 4256 total number of charged atoms : 4101 net assigned charge : -7.499957 assigned positive charge : 639.4351 centred at (gu) : 83.29417 89.46756 91.35532 assigned negative charge : -646.9375 centred at (gu) : 83.46954 89.71494 91.46911 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 77464 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30255 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20889 mr = 55620 m= 1819 mr = 14167 m= 48 mr = 841 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 5707 time to turn everything in is 0.6200000 number of dielectric boundary points 29592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 360 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 31180 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) : 0.5258028 object centre at (A) : 32.09600 13.79650 12.13950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0144283E-02 -1.1867012E-02 midg,1,midg; midg,igrid,midg -4.3049990E-03 -1.1782398E-02 1,midg,midg; igrid,midg,midg 1.9326473E-02 -7.5418721E-03 gauss-seidel spectral radius is 0.9981371 estimated iterations to convergence 184 setup time was (sec) 0.9300000 now iterating at: 11:38:49 rms-change max change #iterations 3.761930 161.1258 at 10iterations 1.548773 46.22474 at 20iterations 0.6399570 22.10253 at 30iterations 0.2640269 10.23154 at 40iterations 0.1092736 3.830379 at 50iterations 4.5133725E-02 1.490368 at 60iterations 1.8662585E-02 0.5767622 at 70iterations 7.7468720E-03 0.2513599 at 80iterations 3.2109818E-03 0.1023216 at 90iterations 1.3339102E-03 4.5926094E-02 at 100iterations 5.5265555E-04 1.8817902E-02 at 110iterations 2.3072399E-04 8.5144043E-03 at 120iterations finished qdiffx linear iterations at : 11:39:01 total time elapsed so far: 12.25000 # loops : 120 mean,max change (kT/e) : 2.3072399E-04 8.5144043E-03 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 11:39:02 12.418u 0.470s 0:13.60 94.7% 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 11:39:02 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 = 4256 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.366112 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): -1.757000 65.94900 ymin,ymax (A): -10.24800 37.84100 zmin,zma (A): -19.70200 43.98100 x,y,z range (A): 67.70599 48.08900 63.68300 scale (grids/A): 2.366112 object centre (A): 32.09600 13.79650 12.13950 number of atom coordinates read : 4256 total number of charged atoms : 4101 net assigned charge : -7.499957 assigned positive charge : 639.4351 centred at (gu) : 79.94101 89.20108 92.03272 assigned negative charge : -646.9375 centred at (gu) : 80.20428 89.57226 92.20336 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 181550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30255 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 76367 mr = 136457 m= 18493 mr = 60553 m= 2700 mr = 13707 m= 124 mr = 1742 m= 0 mr = 35 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 19360 time to turn everything in is 1.540000 number of dielectric boundary points 66740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 32740 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) : 1.577408 object centre at (A) : 32.09600 13.79650 12.13950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2571856 -0.2371566 midg,1,midg; midg,igrid,midg -8.7906465E-02 -0.1686999 1,midg,midg; igrid,midg,midg 0.5414180 -0.3970960 gauss-seidel spectral radius is 0.9991350 estimated iterations to convergence 269 setup time was (sec) 1.890000 now iterating at: 11:39:04 rms-change max change #iterations 9.790037 455.2827 at 10iterations 5.453403 145.5660 at 20iterations 3.026389 63.85095 at 30iterations 1.679002 32.20745 at 40iterations 0.9273594 17.88864 at 50iterations 0.5118141 10.16034 at 60iterations 0.2827042 6.621176 at 70iterations 0.1555476 2.854479 at 80iterations 8.5487477E-02 1.733903 at 90iterations 4.7058452E-02 0.8264866 at 100iterations 2.5846915E-02 0.4814377 at 110iterations 1.4226426E-02 0.2773552 at 120iterations 7.8227445E-03 0.1457024 at 130iterations 4.3002521E-03 8.0690384E-02 at 140iterations 2.3681268E-03 4.8187256E-02 at 150iterations 1.3008798E-03 2.2396088E-02 at 160iterations 7.1605342E-04 1.4888763E-02 at 170iterations 3.9441261E-04 7.2860718E-03 at 180iterations finished qdiffx linear iterations at : 11:39:22 total time elapsed so far: 19.93000 # loops : 180 mean,max change (kT/e) : 3.9441261E-04 7.2860718E-03 energy calculations done at 19.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.10000 DelPhi exited at 11:39:23 20.107u 0.491s 0:21.02 97.9% 0+0k 0+0io 0pf+0w