Mon Oct 10 10:21:10 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 10:21:10 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 !!! WARNING: ASL 103 has a net charge of -0.1000 !!! WARNING: HIT 235 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5771538 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): 16.29900 75.06300 ymin,ymax (A): -45.00000 6.076000 zmin,zma (A): 9.735000 71.41700 x,y,z range (A): 58.76400 51.07600 61.68200 scale (grids/A): 0.5771538 object centre (A): 45.68100 -19.46200 40.57600 number of atom coordinates read : 2896 total number of charged atoms : 2746 net assigned charge : 7.914028 assigned positive charge : 425.5298 centred at (gu) : 92.20713 89.29600 88.78122 assigned negative charge : -417.6163 centred at (gu) : 92.45499 89.34521 88.69453 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6572 nv = 96 ne = 84 npr = 55245 no. pairs analyzed = 55245 no. exposed pairs = 4530 no. arc points = 32671 no. surface atoms = 1488 nbur = 1408 mkacc time = 9.9999994E-02 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= 322 mr = 2798 m= 0 mr = 10 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3212 ## 393 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8226 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7897585E-11 2.4778399E-09 midg,1,midg; midg,igrid,midg 3.0654834E-09 6.6015404E-10 1,midg,midg; igrid,midg,midg 3.6899173E-09 -5.3167408E-09 gauss-seidel spectral radius is 0.9845228 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 10:21:10 rms-change max change #iterations 9.3918376E-02 16.37421 at 10iterations 7.1647507E-03 1.291680 at 20iterations 5.5718614E-04 8.6021423E-02 at 30iterations 5.1838302E-05 1.0831833E-02 at 40iterations 7.9900665E-06 1.3771057E-03 at 50iterations finished qdiffx linear iterations at : 10:21:13 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 7.9900665E-06 1.3771057E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 10:21:14 3.427u 0.177s 0:03.96 90.6% 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 10:21:14 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 !!! WARNING: ASL 103 has a net charge of -0.1000 !!! WARNING: HIT 235 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: 1.731461 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): 16.29900 75.06300 ymin,ymax (A): -45.00000 6.076000 zmin,zma (A): 9.735000 71.41700 x,y,z range (A): 58.76400 51.07600 61.68200 scale (grids/A): 1.731461 object centre (A): 45.68100 -19.46200 40.57600 number of atom coordinates read : 2896 total number of charged atoms : 2746 net assigned charge : 7.914028 assigned positive charge : 425.5298 centred at (gu) : 96.62070 87.88734 86.34306 assigned negative charge : -417.6163 centred at (gu) : 97.36463 88.03548 86.08348 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32671 grid for indexing accessible points = 1.400000 m= 22264 mr = 41330 m= 2954 mr = 14055 m= 119 mr = 1372 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 38054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21273 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) : 0.5771538 object centre at (A) : 45.68100 -19.46200 40.57600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2586898E-03 3.9443430E-02 midg,1,midg; midg,igrid,midg 6.3218768E-03 1.0537132E-02 1,midg,midg; igrid,midg,midg 2.6559411E-02 2.8185651E-04 gauss-seidel spectral radius is 0.9984116 estimated iterations to convergence 199 setup time was (sec) 0.5800000 now iterating at: 10:21:14 rms-change max change #iterations 3.662421 182.0868 at 10iterations 1.598466 58.19141 at 20iterations 0.7044100 27.35664 at 30iterations 0.3078202 10.40641 at 40iterations 0.1354735 4.922165 at 50iterations 5.9599772E-02 2.313152 at 60iterations 2.6112780E-02 0.8911085 at 70iterations 1.1442848E-02 0.4101467 at 80iterations 5.0715772E-03 0.1711197 at 90iterations 2.2186113E-03 8.0947876E-02 at 100iterations 9.7671791E-04 3.6785126E-02 at 110iterations 4.3093265E-04 1.5144348E-02 at 120iterations finished qdiffx linear iterations at : 10:21:22 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 4.3093265E-04 1.5144348E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 10:21:22 7.855u 0.204s 0:08.43 95.4% 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 10:21:22 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 !!! WARNING: ASL 103 has a net charge of -0.1000 !!! WARNING: HIT 235 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: 2.597192 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): 16.29900 75.06300 ymin,ymax (A): -45.00000 6.076000 zmin,zma (A): 9.735000 71.41700 x,y,z range (A): 58.76400 51.07600 61.68200 scale (grids/A): 2.597192 object centre (A): 45.68100 -19.46200 40.57600 number of atom coordinates read : 2896 total number of charged atoms : 2746 net assigned charge : 7.914028 assigned positive charge : 425.5298 centred at (gu) : 99.93095 86.83084 84.51443 assigned negative charge : -417.6163 centred at (gu) : 101.0469 87.05303 84.12507 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 160330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32671 grid for indexing accessible points = 1.400000 m= 72233 mr = 102429 m= 24310 mr = 53197 m= 4826 mr = 17473 m= 442 mr = 2980 m= 24 mr = 177 m= 0 mr = 4 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 85905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 21955 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) : 1.731461 object centre at (A) : 45.68100 -19.46200 40.57600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4373760E-02 0.7816104 midg,1,midg; midg,igrid,midg -2.2074254E-02 0.1240743 1,midg,midg; igrid,midg,midg 0.4044748 6.6456553E-03 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 1.120000 now iterating at: 10:21:24 rms-change max change #iterations 9.484420 303.0402 at 10iterations 5.595955 190.5346 at 20iterations 3.257310 81.36113 at 30iterations 1.885945 45.02269 at 40iterations 1.083184 25.01091 at 50iterations 0.6228243 15.28917 at 60iterations 0.3562415 7.764003 at 70iterations 0.2039249 4.977426 at 80iterations 0.1161848 2.379830 at 90iterations 6.6177562E-02 1.456186 at 100iterations 3.7654124E-02 0.8539743 at 110iterations 2.1390270E-02 0.4557819 at 120iterations 1.2170891E-02 0.2698956 at 130iterations 6.9021629E-03 0.1527061 at 140iterations 3.9196527E-03 8.5838318E-02 at 150iterations 2.2263529E-03 4.3710709E-02 at 160iterations 1.2646123E-03 2.5310516E-02 at 170iterations 7.1741216E-04 1.4076650E-02 at 180iterations finished qdiffx linear iterations at : 10:21:35 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 7.1741216E-04 1.4076650E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 10:21:36 12.803u 0.222s 0:13.31 97.8% 0+0k 0+0io 0pf+0w