Wed Feb 15 08:55:43 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:44 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 = 4070 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: 0.5035218 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): -8.484000 62.21800 ymin,ymax (A): 49.10600 109.4450 zmin,zma (A): 65.22300 112.9220 x,y,z range (A): 70.70200 60.33900 47.69901 scale (grids/A): 0.5035218 object centre (A): 26.86700 79.27550 89.07250 number of atom coordinates read : 4070 total number of charged atoms : 3924 net assigned charge : -1.999980 assigned positive charge : 612.2617 centred at (gu) : 89.37930 87.93157 89.42312 assigned negative charge : -614.2648 centred at (gu) : 89.51069 87.91666 89.50378 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6469 nv = 96 ne = 84 npr = 82048 no. pairs analyzed = 82048 no. exposed pairs = 5202 no. arc points = 36452 no. surface atoms = 1752 nbur = 2318 mkacc time = 0.1700000 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 = 1.708000 m= 243 mr = 3215 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3524 ## 544 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8771 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2662005E-10 -1.3284843E-10 midg,1,midg; midg,igrid,midg -8.1074210E-11 9.8060579E-13 1,midg,midg; igrid,midg,midg 2.2335712E-10 -2.0332418E-10 gauss-seidel spectral radius is 0.9797866 estimated iterations to convergence 58 setup time was (sec) 0.6300000 now iterating at: 08:55:44 rms-change max change #iterations 5.6446135E-02 9.267637 at 10iterations 3.1480137E-03 0.6343689 at 20iterations 2.2412758E-04 3.8867950E-02 at 30iterations 2.9553599E-05 4.0283203E-03 at 40iterations 5.2950272E-06 7.3051453E-04 at 50iterations finished qdiffx linear iterations at : 08:55:47 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 5.2950272E-06 7.3051453E-04 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 08:55:47 3.262u 0.149s 0:03.71 91.6% 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 Wed Feb 15 2012 at 08:55:48 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 = 4070 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: 1.510565 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): -8.484000 62.21800 ymin,ymax (A): 49.10600 109.4450 zmin,zma (A): 65.22300 112.9220 x,y,z range (A): 70.70200 60.33900 47.69901 scale (grids/A): 1.510565 object centre (A): 26.86700 79.27550 89.07250 number of atom coordinates read : 4070 total number of charged atoms : 3924 net assigned charge : -1.999980 assigned positive charge : 612.2617 centred at (gu) : 88.13656 83.79314 88.26823 assigned negative charge : -614.2648 centred at (gu) : 88.53170 83.74957 88.51094 start vw surface at 0.2100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36452 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 20130 mr = 49211 m= 1526 mr = 13115 m= 23 mr = 579 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 304 time to turn everything in is 0.5500000 number of dielectric boundary points 32667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 501 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 29385 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) : 0.5035218 object centre at (A) : 26.86700 79.27550 89.07250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2105051E-03 -2.3743913E-03 midg,1,midg; midg,igrid,midg -7.8106560E-03 -3.8337475E-03 1,midg,midg; igrid,midg,midg 4.4406086E-02 9.3194591E-03 gauss-seidel spectral radius is 0.9979702 estimated iterations to convergence 176 setup time was (sec) 0.8100000 now iterating at: 08:55:49 rms-change max change #iterations 3.340866 151.6385 at 10iterations 1.323997 55.20110 at 20iterations 0.5245399 18.77757 at 30iterations 0.2087759 7.613066 at 40iterations 8.3074406E-02 3.213883 at 50iterations 3.3164173E-02 1.183527 at 60iterations 1.3138641E-02 0.4505024 at 70iterations 5.2225315E-03 0.2146759 at 80iterations 2.0830350E-03 7.8361511E-02 at 90iterations 8.3208521E-04 2.7309418E-02 at 100iterations 3.3069093E-04 1.1293411E-02 at 110iterations 1.3287971E-04 4.8360825E-03 at 120iterations finished qdiffx linear iterations at : 08:55:55 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 1.3287971E-04 4.8360825E-03 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 08:55:56 7.098u 0.206s 0:08.08 90.2% 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 Wed Feb 15 2012 at 08:55:56 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 = 4070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.265848 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): -8.484000 62.21800 ymin,ymax (A): 49.10600 109.4450 zmin,zma (A): 65.22300 112.9220 x,y,z range (A): 70.70200 60.33900 47.69901 scale (grids/A): 2.265848 object centre (A): 26.86700 79.27550 89.07250 number of atom coordinates read : 4070 total number of charged atoms : 3924 net assigned charge : -1.999980 assigned positive charge : 612.2617 centred at (gu) : 87.20456 80.68944 87.40198 assigned negative charge : -614.2648 centred at (gu) : 87.79740 80.62434 87.76633 start vw surface at 0.1800000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 172576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36452 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 73510 mr = 121373 m= 17024 mr = 56588 m= 1972 mr = 12123 m= 57 mr = 1180 m= 0 mr = 12 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 1053 time to turn everything in is 1.190000 number of dielectric boundary points 73863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 31291 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) : 1.510565 object centre at (A) : 26.86700 79.27550 89.07250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6173718E-02 -4.9097918E-02 midg,1,midg; midg,igrid,midg -0.1133511 -4.9055532E-02 1,midg,midg; igrid,midg,midg 0.9771339 0.2164365 gauss-seidel spectral radius is 0.9990944 estimated iterations to convergence 263 setup time was (sec) 1.500000 now iterating at: 08:55:57 rms-change max change #iterations 9.161391 317.8543 at 10iterations 5.128149 148.0132 at 20iterations 2.851290 95.46812 at 30iterations 1.579035 44.17743 at 40iterations 0.8672252 20.93540 at 50iterations 0.4760359 11.24208 at 60iterations 0.2605925 6.171989 at 70iterations 0.1427321 3.102669 at 80iterations 7.7847376E-02 1.748852 at 90iterations 4.2425852E-02 0.9900093 at 100iterations 2.3053536E-02 0.5044250 at 110iterations 1.2526306E-02 0.2600746 at 120iterations 6.8200654E-03 0.1471901 at 130iterations 3.7025786E-03 8.0993652E-02 at 140iterations 2.0091303E-03 3.8773894E-02 at 150iterations 1.0911035E-03 2.3513794E-02 at 160iterations 5.9216912E-04 1.2203217E-02 at 170iterations 3.2107643E-04 7.1449280E-03 at 180iterations finished qdiffx linear iterations at : 08:56:08 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 3.2107643E-04 7.1449280E-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) 12.42000 DelPhi exited at 08:56:09 12.424u 0.202s 0:13.77 91.6% 0+0k 0+0io 0pf+0w