Mon Oct 10 17:04:05 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 Mon Oct 10 2011 at 17:04:05 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4771 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5115898 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): -18.52700 36.93500 ymin,ymax (A): -30.67100 34.16300 zmin,zma (A): -4.113000 65.47400 x,y,z range (A): 55.46200 64.83400 69.58700 scale (grids/A): 0.5115898 object centre (A): 9.204000 1.746001 30.68050 number of atom coordinates read : 4771 total number of charged atoms : 4521 net assigned charge : 7.706036 assigned positive charge : 717.3005 centred at (gu) : 90.21629 90.42339 88.41455 assigned negative charge : -709.5988 centred at (gu) : 90.10588 90.48103 88.37526 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7965 nv = 96 ne = 84 npr = 95942 no. pairs analyzed = 95942 no. exposed pairs = 6085 no. arc points = 42323 no. surface atoms = 2024 nbur = 2747 mkacc time = 0.2100000 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 = 1.652000 m= 269 mr = 4072 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4032 ## 555 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10481 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2320800E-11 1.4652586E-10 midg,1,midg; midg,igrid,midg 2.4114019E-10 -4.5065261E-11 1,midg,midg; igrid,midg,midg -1.7366016E-10 4.3160664E-10 gauss-seidel spectral radius is 0.9804631 estimated iterations to convergence 59 setup time was (sec) 0.6600000 now iterating at: 17:04:06 rms-change max change #iterations 6.8473741E-02 10.46113 at 10iterations 4.1442658E-03 0.5445290 at 20iterations 5.3440512E-04 7.9635620E-02 at 30iterations 2.0145199E-04 3.2472372E-02 at 40iterations 8.5033935E-05 1.3687730E-02 at 50iterations finished qdiffx linear iterations at : 17:04:08 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 8.5033935E-05 1.3687730E-02 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 17:04:09 3.234u 0.164s 0:04.33 78.2% 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 Mon Oct 10 2011 at 17:04:09 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4771 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.534769 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): -18.52700 36.93500 ymin,ymax (A): -30.67100 34.16300 zmin,zma (A): -4.113000 65.47400 x,y,z range (A): 55.46200 64.83400 69.58700 scale (grids/A): 1.534769 object centre (A): 9.204000 1.746001 30.68050 number of atom coordinates read : 4771 total number of charged atoms : 4521 net assigned charge : 7.706036 assigned positive charge : 717.3005 centred at (gu) : 90.64787 91.26858 85.24223 assigned negative charge : -709.5988 centred at (gu) : 90.31743 91.44284 85.12572 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 90242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42323 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25660 mr = 61800 m= 2189 mr = 16880 m= 45 mr = 889 m= 0 mr = 4 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.6200000 number of dielectric boundary points 38563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 534 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 34026 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) : 0.5115898 object centre at (A) : 9.204000 1.746001 30.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8643887E-03 2.2486376E-02 midg,1,midg; midg,igrid,midg 1.0569977E-02 -1.0950904E-02 1,midg,midg; igrid,midg,midg -1.6322085E-03 1.2711994E-02 gauss-seidel spectral radius is 0.9981242 estimated iterations to convergence 183 setup time was (sec) 0.8900000 now iterating at: 17:04:11 rms-change max change #iterations 3.803509 146.4090 at 10iterations 1.562029 54.00790 at 20iterations 0.6413867 20.70546 at 30iterations 0.2645772 8.758107 at 40iterations 0.1089145 3.542788 at 50iterations 4.4934109E-02 1.570424 at 60iterations 1.8508621E-02 0.5936241 at 70iterations 7.6789963E-03 0.2419472 at 80iterations 3.2076510E-03 0.1163607 at 90iterations 1.3738411E-03 4.8002243E-02 at 100iterations 6.2530686E-04 2.1642208E-02 at 110iterations 3.2129718E-04 1.2522697E-02 at 120iterations finished qdiffx linear iterations at : 17:04:16 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 3.2129718E-04 1.2522697E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 17:04:17 7.041u 0.163s 0:07.74 93.0% 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 Mon Oct 10 2011 at 17:04:17 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4771 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.302154 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): -18.52700 36.93500 ymin,ymax (A): -30.67100 34.16300 zmin,zma (A): -4.113000 65.47400 x,y,z range (A): 55.46200 64.83400 69.58700 scale (grids/A): 2.302154 object centre (A): 9.204000 1.746001 30.68050 number of atom coordinates read : 4771 total number of charged atoms : 4521 net assigned charge : 7.706036 assigned positive charge : 717.3005 centred at (gu) : 90.97133 91.90275 82.86303 assigned negative charge : -709.5988 centred at (gu) : 90.47613 92.16419 82.68846 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 210199 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42323 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93020 mr = 152012 m= 22924 mr = 72282 m= 3164 mr = 16107 m= 162 mr = 1851 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 241 time to turn everything in is 1.460000 number of dielectric boundary points 87151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 36065 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) : 1.534769 object centre at (A) : 9.204000 1.746001 30.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1354859 0.5322891 midg,1,midg; midg,igrid,midg 0.1620129 -0.2780260 1,midg,midg; igrid,midg,midg -2.6491389E-02 0.1803361 gauss-seidel spectral radius is 0.9991682 estimated iterations to convergence 274 setup time was (sec) 1.750000 now iterating at: 17:04:19 rms-change max change #iterations 10.33308 284.0957 at 10iterations 5.933630 162.6196 at 20iterations 3.384717 79.05662 at 30iterations 1.920542 40.61735 at 40iterations 1.085504 23.97009 at 50iterations 0.6120790 12.57172 at 60iterations 0.3434357 7.171153 at 70iterations 0.1925024 4.158890 at 80iterations 0.1078777 2.089688 at 90iterations 6.0201064E-02 1.386393 at 100iterations 3.3609558E-02 0.6224632 at 110iterations 1.8796807E-02 0.3964920 at 120iterations 1.0488895E-02 0.2019860 at 130iterations 5.8559887E-03 0.1102629 at 140iterations 3.2778445E-03 7.1452618E-02 at 150iterations 1.8359027E-03 3.8709641E-02 at 160iterations 1.0372457E-03 1.9844055E-02 at 170iterations 5.9457542E-04 1.2464523E-02 at 180iterations finished qdiffx linear iterations at : 17:04:29 total time elapsed so far: 11.41000 # loops : 180 mean,max change (kT/e) : 5.9457542E-04 1.2464523E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.57000 DelPhi exited at 17:04:29 11.573u 0.179s 0:12.11 96.9% 0+0k 0+0io 0pf+0w