Mon Oct 10 17:04:21 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 17:04:22 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 !!! WARNING: HIR 148 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= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.5743881 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): -23.18600 26.92700 ymin,ymax (A): -63.87100 -3.530000 zmin,zma (A): -58.06300 3.916000 x,y,z range (A): 50.11300 60.34100 61.97900 scale (grids/A): 0.5743881 object centre (A): 1.870501 -33.70050 -27.07350 number of atom coordinates read : 3108 total number of charged atoms : 2955 net assigned charge : -2.485967 assigned positive charge : 467.2738 centred at (gu) : 91.30943 89.68212 91.00288 assigned negative charge : -469.7610 centred at (gu) : 91.35121 89.86707 91.07537 start vw surface at 0.3000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 6601 nv = 96 ne = 84 npr = 63406 no. pairs analyzed = 63406 no. exposed pairs = 3961 no. arc points = 27891 no. surface atoms = 1341 nbur = 1767 mkacc time = 0.1800000 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= 251 mr = 3376 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.5300000 number of dielectric boundary points 3461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2834 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 8531 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4783829E-10 -2.3279467E-09 midg,1,midg; midg,igrid,midg 3.2959111E-09 -3.7639012E-09 1,midg,midg; igrid,midg,midg 2.6828784E-10 -1.6844319E-09 gauss-seidel spectral radius is 0.9843689 estimated iterations to convergence 66 setup time was (sec) 0.8300000 now iterating at: 17:04:23 rms-change max change #iterations 9.6657835E-02 17.55147 at 10iterations 7.3077334E-03 1.020592 at 20iterations 5.6072662E-04 7.7747345E-02 at 30iterations 4.8291113E-05 8.1405640E-03 at 40iterations 5.5853689E-06 1.1096001E-03 at 50iterations finished qdiffx linear iterations at : 17:04:26 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 5.5853689E-06 1.1096001E-03 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 17:04:27 4.471u 0.198s 0:05.37 86.7% 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 Mon Oct 10 2011 at 17:04:27 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 !!! WARNING: HIR 148 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.723164 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): -23.18600 26.92700 ymin,ymax (A): -63.87100 -3.530000 zmin,zma (A): -58.06300 3.916000 x,y,z range (A): 50.11300 60.34100 61.97900 scale (grids/A): 1.723164 object centre (A): 1.870501 -33.70050 -27.07350 number of atom coordinates read : 3108 total number of charged atoms : 2955 net assigned charge : -2.485967 assigned positive charge : 467.2738 centred at (gu) : 93.92729 89.04524 93.00759 assigned negative charge : -469.7610 centred at (gu) : 94.05317 89.60084 93.22575 start vw surface at 0.2400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 73011 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27891 grid for indexing accessible points = 1.400000 m= 21674 mr = 49241 m= 2152 mr = 14518 m= 64 mr = 1052 m= 0 mr = 8 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1135 time to turn everything in is 0.7100000 number of dielectric boundary points 32082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22867 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) : 0.5743881 object centre at (A) : 1.870501 -33.70050 -27.07350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9356156E-04 -1.3294772E-02 midg,1,midg; midg,igrid,midg 1.8727442E-02 -3.5112977E-02 1,midg,midg; igrid,midg,midg 1.5920209E-04 -9.2375716E-03 gauss-seidel spectral radius is 0.9983867 estimated iterations to convergence 198 setup time was (sec) 1.060000 now iterating at: 17:04:28 rms-change max change #iterations 3.850798 181.9953 at 10iterations 1.689280 67.03110 at 20iterations 0.7378747 26.17279 at 30iterations 0.3222347 11.98400 at 40iterations 0.1414970 4.537954 at 50iterations 6.1965078E-02 2.134002 at 60iterations 2.7178371E-02 1.089569 at 70iterations 1.1862911E-02 0.3897820 at 80iterations 5.2231699E-03 0.1750116 at 90iterations 2.2899176E-03 7.6625824E-02 at 100iterations 1.0056574E-03 3.5900116E-02 at 110iterations 4.4241457E-04 1.4526367E-02 at 120iterations finished qdiffx linear iterations at : 17:04:36 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 4.4241457E-04 1.4526367E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 17:04:37 9.476u 0.258s 0:10.43 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 Mon Oct 10 2011 at 17:04:38 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 !!! WARNING: HIR 148 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.584746 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): -23.18600 26.92700 ymin,ymax (A): -63.87100 -3.530000 zmin,zma (A): -58.06300 3.916000 x,y,z range (A): 50.11300 60.34100 61.97900 scale (grids/A): 2.584746 object centre (A): 1.870501 -33.70050 -27.07350 number of atom coordinates read : 3108 total number of charged atoms : 2955 net assigned charge : -2.485967 assigned positive charge : 467.2738 centred at (gu) : 95.89076 88.56750 94.51118 assigned negative charge : -469.7610 centred at (gu) : 96.07973 89.40121 94.83848 start vw surface at 0.2800000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 169745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27891 grid for indexing accessible points = 1.400000 m= 75091 mr = 120547 m= 20918 mr = 58707 m= 3338 mr = 15495 m= 244 mr = 2159 m= 4 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 3950 time to turn everything in is 1.700000 number of dielectric boundary points 72317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 23627 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) : 1.723164 object centre at (A) : 1.870501 -33.70050 -27.07350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1153956E-02 -0.1398782 midg,1,midg; midg,igrid,midg 0.4180357 -0.3540136 1,midg,midg; igrid,midg,midg 6.4196093E-03 -0.1251350 gauss-seidel spectral radius is 0.9992048 estimated iterations to convergence 280 setup time was (sec) 2.100000 now iterating at: 17:04:40 rms-change max change #iterations 9.709238 277.7410 at 10iterations 5.559245 145.4369 at 20iterations 3.160689 70.90497 at 30iterations 1.795467 37.80140 at 40iterations 1.018412 21.19360 at 50iterations 0.5766688 12.00403 at 60iterations 0.3255023 6.393622 at 70iterations 0.1837561 3.819092 at 80iterations 0.1036928 2.029386 at 90iterations 5.8477879E-02 1.131458 at 100iterations 3.2947175E-02 0.6343460 at 110iterations 1.8576037E-02 0.3593237 at 120iterations 1.0448235E-02 0.1925392 at 130iterations 5.8974042E-03 0.1135616 at 140iterations 3.3133917E-03 6.5949440E-02 at 150iterations 1.8713517E-03 3.6506772E-02 at 160iterations 1.0561000E-03 2.1110535E-02 at 170iterations 5.9666904E-04 1.1306286E-02 at 180iterations finished qdiffx linear iterations at : 17:04:53 total time elapsed so far: 15.08000 # loops : 180 mean,max change (kT/e) : 5.9666904E-04 1.1306286E-02 energy calculations done at 15.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.32000 DelPhi exited at 17:04:54 15.318u 0.290s 0:16.65 93.6% 0+0k 0+0io 0pf+0w