Sat Oct 8 11:43:15 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 11:43:15 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 = 2427 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5763968 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): -27.23000 22.06600 ymin,ymax (A): -37.63300 24.13000 zmin,zma (A): -49.43400 6.217000 x,y,z range (A): 49.29600 61.76300 55.65100 scale (grids/A): 0.5763968 object centre (A): -2.582000 -6.751501 -21.60850 number of atom coordinates read : 2427 total number of charged atoms : 2279 net assigned charge : -2.499994 assigned positive charge : 351.5960 centred at (gu) : 89.46886 92.18398 92.11212 assigned negative charge : -354.0964 centred at (gu) : 89.48759 92.17236 92.03020 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5377 nv = 96 ne = 84 npr = 48395 no. pairs analyzed = 48395 no. exposed pairs = 3288 no. arc points = 23362 no. surface atoms = 1105 nbur = 1322 mkacc time = 0.1600000 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 = 1.484000 m= 230 mr = 2634 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 2953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 6778 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0889184E-09 1.2484872E-09 midg,1,midg; midg,igrid,midg -4.1915296E-10 -5.4502758E-10 1,midg,midg; igrid,midg,midg -2.5130378E-10 -7.0742745E-10 gauss-seidel spectral radius is 0.9844275 estimated iterations to convergence 66 setup time was (sec) 0.6600000 now iterating at: 11:43:16 rms-change max change #iterations 8.2812041E-02 15.64249 at 10iterations 6.4397901E-03 1.079578 at 20iterations 4.9905438E-04 8.0287457E-02 at 30iterations 4.1993368E-05 7.9612732E-03 at 40iterations 4.9468867E-06 7.8964233E-04 at 50iterations finished qdiffx linear iterations at : 11:43:20 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 4.9468867E-06 7.8964233E-04 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 11:43:20 4.461u 0.432s 0:05.17 94.5% 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 Sat Oct 8 2011 at 11:43:20 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 = 2427 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.729190 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): -27.23000 22.06600 ymin,ymax (A): -37.63300 24.13000 zmin,zma (A): -49.43400 6.217000 x,y,z range (A): 49.29600 61.76300 55.65100 scale (grids/A): 1.729190 object centre (A): -2.582000 -6.751501 -21.60850 number of atom coordinates read : 2427 total number of charged atoms : 2279 net assigned charge : -2.499994 assigned positive charge : 351.5960 centred at (gu) : 88.40603 96.55139 96.33583 assigned negative charge : -354.0964 centred at (gu) : 88.46249 96.51656 96.09023 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 58697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23362 grid for indexing accessible points = 1.400000 m= 18116 mr = 38298 m= 1991 mr = 12257 m= 63 mr = 1002 m= 0 mr = 16 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 177 time to turn everything in is 0.6200000 number of dielectric boundary points 27294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17722 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) : 0.5763968 object centre at (A) : -2.582000 -6.751501 -21.60850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7980824E-03 1.0000597E-02 midg,1,midg; midg,igrid,midg 1.0926359E-03 -1.4957679E-03 1,midg,midg; igrid,midg,midg -5.2966624E-03 -4.2660865E-03 gauss-seidel spectral radius is 0.9983301 estimated iterations to convergence 194 setup time was (sec) 0.9500000 now iterating at: 11:43:21 rms-change max change #iterations 3.294831 152.4814 at 10iterations 1.416856 64.73973 at 20iterations 0.6117416 23.94891 at 30iterations 0.2627850 10.73767 at 40iterations 0.1130374 4.050446 at 50iterations 4.8867881E-02 1.913985 at 60iterations 2.1139411E-02 0.7750225 at 70iterations 9.0891402E-03 0.3570518 at 80iterations 3.9304639E-03 0.1415806 at 90iterations 1.6950738E-03 6.0486317E-02 at 100iterations 7.3554082E-04 2.5791883E-02 at 110iterations 3.1701240E-04 1.1764526E-02 at 120iterations finished qdiffx linear iterations at : 11:43:30 total time elapsed so far: 9.790000 # loops : 120 mean,max change (kT/e) : 3.1701240E-04 1.1764526E-02 energy calculations done at 9.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.01000 DelPhi exited at 11:43:31 10.012u 0.480s 0:10.74 97.6% 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 Sat Oct 8 2011 at 11:43:31 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 = 2427 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.593786 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): -27.23000 22.06600 ymin,ymax (A): -37.63300 24.13000 zmin,zma (A): -49.43400 6.217000 x,y,z range (A): 49.29600 61.76300 55.65100 scale (grids/A): 2.593786 object centre (A): -2.582000 -6.751501 -21.60850 number of atom coordinates read : 2427 total number of charged atoms : 2279 net assigned charge : -2.499994 assigned positive charge : 351.5960 centred at (gu) : 87.60886 99.82692 99.50365 assigned negative charge : -354.0964 centred at (gu) : 87.69364 99.77480 99.13527 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 136063 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23362 grid for indexing accessible points = 1.400000 m= 61221 mr = 93791 m= 18322 mr = 47657 m= 3151 mr = 13771 m= 223 mr = 2040 m= 5 mr = 115 m= 0 mr = 2 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 627 time to turn everything in is 1.500000 number of dielectric boundary points 61609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 18221 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) : 1.729190 object centre at (A) : -2.582000 -6.751501 -21.60850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1179204 0.2035113 midg,1,midg; midg,igrid,midg 1.5835796E-02 0.1060442 1,midg,midg; igrid,midg,midg -4.9348161E-02 -6.9164908E-03 gauss-seidel spectral radius is 0.9991682 estimated iterations to convergence 274 setup time was (sec) 1.880000 now iterating at: 11:43:33 rms-change max change #iterations 8.408118 285.8405 at 10iterations 4.825511 127.6952 at 20iterations 2.739966 72.82794 at 30iterations 1.546937 43.61269 at 40iterations 0.8718490 21.91403 at 50iterations 0.4878283 10.85577 at 60iterations 0.2731049 6.056961 at 70iterations 0.1526311 3.131638 at 80iterations 8.5082583E-02 1.837911 at 90iterations 4.7472950E-02 0.9780025 at 100iterations 2.6421087E-02 0.5993809 at 110iterations 1.4735233E-02 0.3310242 at 120iterations 8.1971604E-03 0.1738434 at 130iterations 4.5530265E-03 0.1046617 at 140iterations 2.5354216E-03 5.7563782E-02 at 150iterations 1.4069095E-03 3.0147552E-02 at 160iterations 7.8433490E-04 1.5447617E-02 at 170iterations 4.3627026E-04 1.0076523E-02 at 180iterations finished qdiffx linear iterations at : 11:43:48 total time elapsed so far: 16.46000 # loops : 180 mean,max change (kT/e) : 4.3627026E-04 1.0076523E-02 energy calculations done at 16.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.67000 DelPhi exited at 11:43:48 16.678u 0.519s 0:17.47 98.3% 0+0k 0+0io 0pf+0w