Tue Oct 11 06:24:42 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+sph2.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 = amb2.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 06:24:42 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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 : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.87370 89.93713 90.39251 assigned negative charge : -304.4261 centred at (gu) : 90.06351 89.91369 90.41960 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 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 0.3100000 number of dielectric boundary points 3424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1553 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7930 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1486584E-08 6.7638567E-08 midg,1,midg; midg,igrid,midg 6.6141226E-08 9.4926399E-08 1,midg,midg; igrid,midg,midg 2.0755182E-07 -4.4471314E-08 gauss-seidel spectral radius is 0.9899747 estimated iterations to convergence 81 setup time was (sec) 0.5800000 now iterating at: 06:24:43 rms-change max change #iterations 0.2184517 31.08754 at 10iterations 2.9080141E-02 3.718903 at 20iterations 4.0835929E-03 0.4871178 at 30iterations 7.2341377E-04 9.7498894E-02 at 40iterations 1.8307783E-04 2.1316528E-02 at 50iterations finished qdiffx linear iterations at : 06:24:46 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 1.8307783E-04 2.1316528E-02 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 06:24:47 4.083u 0.282s 0:04.68 93.1% 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 06:24:47 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-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 : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.62124 89.81148 91.17753 assigned negative charge : -304.4261 centred at (gu) : 90.19072 89.74120 91.25884 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 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 0.7000000 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 0.8400000 number of grid points assigned charge 15285 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 5.8257572E-02 7.0846140E-02 midg,1,midg; midg,igrid,midg 4.4557289E-03 2.9557966E-02 1,midg,midg; igrid,midg,midg 4.9280424E-02 7.6405420E-03 gauss-seidel spectral radius is 0.9988664 estimated iterations to convergence 235 setup time was (sec) 1.010000 now iterating at: 06:24:48 rms-change max change #iterations 4.721214 186.3054 at 10iterations 2.354171 81.89299 at 20iterations 1.187885 36.86412 at 30iterations 0.5943013 19.10317 at 40iterations 0.2991277 8.262513 at 50iterations 0.1505076 4.682047 at 60iterations 7.5634457E-02 2.262227 at 70iterations 3.7931796E-02 1.083277 at 80iterations 1.9169405E-02 0.5622559 at 90iterations 9.7778980E-03 0.2834473 at 100iterations 4.9846754E-03 0.1436939 at 110iterations 2.5958598E-03 7.4125290E-02 at 120iterations finished qdiffx linear iterations at : 06:24:57 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 2.5958598E-03 7.4125290E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 06:24:57 9.657u 0.311s 0:10.25 97.1% 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 06:24:57 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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 : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.43185 89.71732 91.76627 assigned negative charge : -304.4261 centred at (gu) : 90.28622 89.61193 91.88844 start vw surface at 0.1500000 fill in re-entrant regions at 1.020000 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 2.470000 number of grid points assigned charge 15384 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 0.4825206 0.6334785 midg,1,midg; midg,igrid,midg -2.3347972E-02 0.2098364 1,midg,midg; igrid,midg,midg 0.3463685 0.1763447 gauss-seidel spectral radius is 0.9993007 estimated iterations to convergence 298 setup time was (sec) 2.650000 now iterating at: 06:25:00 rms-change max change #iterations 10.41496 434.4825 at 10iterations 6.199846 138.8677 at 20iterations 3.665595 66.02772 at 30iterations 2.165886 39.37328 at 40iterations 1.278017 23.59457 at 50iterations 0.7529433 13.83373 at 60iterations 0.4442995 8.506079 at 70iterations 0.2616197 5.518763 at 80iterations 0.1535238 2.784152 at 90iterations 9.0518586E-02 1.559204 at 100iterations 5.3481724E-02 0.8880615 at 110iterations 3.1744156E-02 0.5395508 at 120iterations 1.9124210E-02 0.3548889 at 130iterations 1.1792778E-02 0.2216721 at 140iterations 7.5281076E-03 0.1355209 at 150iterations 5.0636078E-03 9.7450256E-02 at 160iterations 3.6090119E-03 6.7466736E-02 at 170iterations 2.7179262E-03 4.8728943E-02 at 180iterations finished qdiffx linear iterations at : 06:25:14 total time elapsed so far: 16.66000 # loops : 180 mean,max change (kT/e) : 2.7179262E-03 4.8728943E-02 energy calculations done at 16.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.84000 DelPhi exited at 06:25:15 16.845u 0.315s 0:17.65 97.1% 0+0k 0+0io 0pf+0w