Mon Oct 10 12:16:12 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 12:16:12 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7511182 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): -23.10600 23.96200 ymin,ymax (A): -7.368000 35.77300 zmin,zma (A): -3.355000 44.04100 x,y,z range (A): 47.06800 43.14100 47.39600 scale (grids/A): 0.7511182 object centre (A): 0.4280005 14.20250 20.34300 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 318.6999 centred at (gu) : 89.69630 90.37242 90.28102 assigned negative charge : -324.9720 centred at (gu) : 89.72920 90.47038 90.47680 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8300 nv = 96 ne = 84 npr = 43706 no. pairs analyzed = 43706 no. exposed pairs = 2739 no. arc points = 19374 no. surface atoms = 932 nbur = 1185 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 674 mr = 4639 m= 7 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2800000 number of dielectric boundary points 4187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1529 ## 103 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0314983E-07 -4.1713051E-07 midg,1,midg; midg,igrid,midg -1.3133730E-08 -2.8501998E-07 1,midg,midg; igrid,midg,midg -1.0152558E-07 -1.7158290E-07 gauss-seidel spectral radius is 0.9907644 estimated iterations to convergence 85 setup time was (sec) 0.5500000 now iterating at: 12:16:13 rms-change max change #iterations 0.2670651 39.55509 at 10iterations 3.7075836E-02 4.668715 at 20iterations 5.1131067E-03 0.7186580 at 30iterations 7.2021177E-04 8.1220627E-02 at 40iterations 9.8705241E-05 1.2399197E-02 at 50iterations finished qdiffx linear iterations at : 12:16:17 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 9.8705241E-05 1.2399197E-02 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 12:16:17 4.587u 0.416s 0:05.50 90.7% 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 12:16:18 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.253355 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): -23.10600 23.96200 ymin,ymax (A): -7.368000 35.77300 zmin,zma (A): -3.355000 44.04100 x,y,z range (A): 47.06800 43.14100 47.39600 scale (grids/A): 2.253355 object centre (A): 0.4280005 14.20250 20.34300 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 318.6999 centred at (gu) : 89.08882 91.11732 90.84302 assigned negative charge : -324.9720 centred at (gu) : 89.18777 91.41119 91.43037 start vw surface at 0.1200000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 86292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19374 grid for indexing accessible points = 1.400000 m= 36484 mr = 59365 m= 8973 mr = 28010 m= 1165 mr = 6424 m= 40 mr = 661 m= 0 mr = 3 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 798 time to turn everything in is 0.7500000 number of dielectric boundary points 38491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 15769 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) : 0.7511182 object centre at (A) : 0.4280005 14.20250 20.34300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1578151E-03 -0.1515755 midg,1,midg; midg,igrid,midg -1.9891832E-02 -3.8969662E-02 1,midg,midg; igrid,midg,midg -1.1296643E-02 -2.6853664E-02 gauss-seidel spectral radius is 0.9989548 estimated iterations to convergence 245 setup time was (sec) 1.090000 now iterating at: 12:16:19 rms-change max change #iterations 5.248869 227.4979 at 10iterations 2.685041 90.99751 at 20iterations 1.379427 41.98502 at 30iterations 0.7081438 20.16579 at 40iterations 0.3662447 9.907957 at 50iterations 0.1880570 5.188589 at 60iterations 9.6494146E-02 2.774979 at 70iterations 4.9853031E-02 1.371053 at 80iterations 2.5518609E-02 0.6679420 at 90iterations 1.3122775E-02 0.3541870 at 100iterations 6.7715137E-03 0.1880493 at 110iterations 3.4829634E-03 9.5277309E-02 at 120iterations finished qdiffx linear iterations at : 12:16:29 total time elapsed so far: 11.17000 # loops : 120 mean,max change (kT/e) : 3.4829634E-03 9.5277309E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.34000 DelPhi exited at 12:16:30 11.347u 0.445s 0:12.24 96.2% 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 12:16:30 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.380032 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): -23.10600 23.96200 ymin,ymax (A): -7.368000 35.77300 zmin,zma (A): -3.355000 44.04100 x,y,z range (A): 47.06800 43.14100 47.39600 scale (grids/A): 3.380032 object centre (A): 0.4280005 14.20250 20.34300 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 318.6999 centred at (gu) : 88.63315 91.67602 91.26443 assigned negative charge : -324.9720 centred at (gu) : 88.78155 92.11679 92.14552 start vw surface at 0.1700000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 198222 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19374 grid for indexing accessible points = 1.400000 m= 109000 mr = 142778 m= 50316 mr = 90379 m= 17507 mr = 42290 m= 4559 mr = 14124 m= 799 mr = 3505 m= 46 mr = 555 m= 0 mr = 12 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 2679 time to turn everything in is 2.400000 number of dielectric boundary points 86806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.550000 number of grid points assigned charge 15824 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) : 2.253355 object centre at (A) : 0.4280005 14.20250 20.34300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2820249E-02 -1.306252 midg,1,midg; midg,igrid,midg -0.1821076 -0.2302951 1,midg,midg; igrid,midg,midg -0.1441219 -0.4112600 gauss-seidel spectral radius is 0.9993285 estimated iterations to convergence 304 setup time was (sec) 2.760000 now iterating at: 12:16:33 rms-change max change #iterations 11.25232 275.6613 at 10iterations 6.626775 112.3101 at 20iterations 3.915317 67.09406 at 30iterations 2.308280 42.56163 at 40iterations 1.359560 21.22082 at 50iterations 0.8011685 12.57947 at 60iterations 0.4721048 7.387691 at 70iterations 0.2781172 4.558921 at 80iterations 0.1637734 2.871796 at 90iterations 9.6430115E-02 1.715149 at 100iterations 5.6696430E-02 0.9651753 at 110iterations 3.3476800E-02 0.5106759 at 120iterations 1.9720903E-02 0.3050208 at 130iterations 1.1608930E-02 0.1856134 at 140iterations 6.8392339E-03 0.1008701 at 150iterations 4.0248805E-03 6.1138153E-02 at 160iterations 2.3742400E-03 4.0016174E-02 at 170iterations 1.4011239E-03 2.3262501E-02 at 180iterations finished qdiffx linear iterations at : 12:16:50 total time elapsed so far: 20.04000 # loops : 180 mean,max change (kT/e) : 1.4011239E-03 2.3262501E-02 energy calculations done at 20.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.23000 DelPhi exited at 12:16:51 20.236u 0.498s 0:21.17 97.8% 0+0k 0+0io 0pf+0w