Sun Oct 9 11:44:17 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 Sun Oct 9 2011 at 11:44:17 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2688 !!! WARNING: HIR 203 has a net charge of 0.5140 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: 0.6584910 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): -6.158000 47.73900 ymin,ymax (A): 8.976001 59.76900 zmin,zma (A): 5.298000 59.36100 x,y,z range (A): 53.89700 50.79300 54.06300 scale (grids/A): 0.6584910 object centre (A): 20.79050 34.37250 32.32950 number of atom coordinates read : 2688 total number of charged atoms : 2620 net assigned charge : 2.014012 assigned positive charge : 404.0050 centred at (gu) : 90.85741 90.23605 91.01544 assigned negative charge : -401.9926 centred at (gu) : 90.88381 90.18793 91.01520 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8354 nv = 96 ne = 84 npr = 50849 no. pairs analyzed = 50849 no. exposed pairs = 3789 no. arc points = 26998 no. surface atoms = 1264 nbur = 1424 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 576 mr = 4336 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2100000 number of dielectric boundary points 4526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2499 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9636 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9863015E-09 6.1148828E-09 midg,1,midg; midg,igrid,midg -4.3524508E-09 1.5081275E-08 1,midg,midg; igrid,midg,midg 8.4752472E-09 -3.9724807E-10 gauss-seidel spectral radius is 0.9880776 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 11:44:17 rms-change max change #iterations 0.1683640 22.42677 at 10iterations 1.7867152E-02 2.654198 at 20iterations 1.8936269E-03 0.2551956 at 30iterations 2.1648014E-04 2.7675152E-02 at 40iterations 4.5391724E-05 7.8382492E-03 at 50iterations finished qdiffx linear iterations at : 11:44:20 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 4.5391724E-05 7.8382492E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 11:44:21 3.416u 0.159s 0:03.86 92.2% 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 Sun Oct 9 2011 at 11:44:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2688 !!! WARNING: HIR 203 has a net charge of 0.5140 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: 1.975473 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): -6.158000 47.73900 ymin,ymax (A): 8.976001 59.76900 zmin,zma (A): 5.298000 59.36100 x,y,z range (A): 53.89700 50.79300 54.06300 scale (grids/A): 1.975473 object centre (A): 20.79050 34.37250 32.32950 number of atom coordinates read : 2688 total number of charged atoms : 2620 net assigned charge : 2.014012 assigned positive charge : 404.0050 centred at (gu) : 92.57127 90.70708 93.04523 assigned negative charge : -401.9926 centred at (gu) : 92.65148 90.56380 93.04549 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 88918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26998 grid for indexing accessible points = 1.400000 m= 33379 mr = 59208 m= 6539 mr = 24020 m= 556 mr = 4154 m= 9 mr = 215 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 41804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20744 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) : 0.6584910 object centre at (A) : 20.79050 34.37250 32.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6119120E-03 2.9529249E-02 midg,1,midg; midg,igrid,midg -5.4019880E-03 2.8868251E-02 1,midg,midg; igrid,midg,midg -1.7994629E-02 -9.3444968E-03 gauss-seidel spectral radius is 0.9987680 estimated iterations to convergence 226 setup time was (sec) 0.6600000 now iterating at: 11:44:21 rms-change max change #iterations 4.709263 182.7017 at 10iterations 2.284793 81.43645 at 20iterations 1.107729 33.16528 at 30iterations 0.5380121 16.10019 at 40iterations 0.2605507 7.680407 at 50iterations 0.1267151 3.651585 at 60iterations 6.1454777E-02 1.796926 at 70iterations 2.9806051E-02 1.004418 at 80iterations 1.4503907E-02 0.3927002 at 90iterations 7.0382934E-03 0.2170773 at 100iterations 3.4173396E-03 9.6636772E-02 at 110iterations 1.6686725E-03 4.8068762E-02 at 120iterations finished qdiffx linear iterations at : 11:44:29 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.6686725E-03 4.8068762E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 11:44:29 7.962u 0.202s 0:08.43 96.7% 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 Sun Oct 9 2011 at 11:44:29 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2688 !!! WARNING: HIR 203 has a net charge of 0.5140 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: 2.963210 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): -6.158000 47.73900 ymin,ymax (A): 8.976001 59.76900 zmin,zma (A): 5.298000 59.36100 x,y,z range (A): 53.89700 50.79300 54.06300 scale (grids/A): 2.963210 object centre (A): 20.79050 34.37250 32.32950 number of atom coordinates read : 2688 total number of charged atoms : 2620 net assigned charge : 2.014012 assigned positive charge : 404.0050 centred at (gu) : 93.85667 91.06046 94.56773 assigned negative charge : -401.9926 centred at (gu) : 93.97724 90.84571 94.56818 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 205083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26998 grid for indexing accessible points = 1.400000 m= 103881 mr = 144166 m= 41860 mr = 82987 m= 12086 mr = 33168 m= 2133 mr = 9095 m= 161 mr = 1425 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 94297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 20960 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) : 1.975473 object centre at (A) : 20.79050 34.37250 32.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5158331E-03 0.3586564 midg,1,midg; midg,igrid,midg 2.6752522E-02 0.3155861 1,midg,midg; igrid,midg,midg -0.2364717 0.1484381 gauss-seidel spectral radius is 0.9993184 estimated iterations to convergence 302 setup time was (sec) 1.400000 now iterating at: 11:44:31 rms-change max change #iterations 11.03400 449.2258 at 10iterations 6.691259 158.6087 at 20iterations 4.033162 80.80453 at 30iterations 2.419846 47.43386 at 40iterations 1.448606 31.35346 at 50iterations 0.8621124 14.90200 at 60iterations 0.5121065 9.400204 at 70iterations 0.3039658 6.445706 at 80iterations 0.1795461 3.138293 at 90iterations 0.1061747 1.885769 at 100iterations 6.2738016E-02 1.063605 at 110iterations 3.7044335E-02 0.6843948 at 120iterations 2.1826696E-02 0.3808327 at 130iterations 1.2900565E-02 0.2290344 at 140iterations 7.6103765E-03 0.1288071 at 150iterations 4.5118430E-03 7.8913689E-02 at 160iterations 2.6758979E-03 4.4574738E-02 at 170iterations 1.6091821E-03 2.8125763E-02 at 180iterations finished qdiffx linear iterations at : 11:44:42 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 1.6091821E-03 2.8125763E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 11:44:43 13.223u 0.201s 0:13.68 98.0% 0+0k 0+0io 0pf+0w