Tue Nov 22 14:20:14 PST 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+sph.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 = amb.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 Tue Nov 22 2011 at 14:20:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6434937 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): -6.129000 34.89800 ymin,ymax (A): -4.037000 49.53700 zmin,zma (A): -24.42000 30.90300 x,y,z range (A): 41.02700 53.57400 55.32300 scale (grids/A): 0.6434937 object centre (A): 14.38450 22.75000 3.241500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 90.90540 92.57582 90.22314 assigned negative charge : -282.8263 centred at (gu) : 90.96925 92.66478 90.17812 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5580 nv = 96 ne = 84 npr = 40320 no. pairs analyzed = 40320 no. exposed pairs = 2400 no. arc points = 17080 no. surface atoms = 817 nbur = 1145 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 299 mr = 3147 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.2100000 number of dielectric boundary points 2689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1732 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9100008E-09 1.3017791E-08 midg,1,midg; midg,igrid,midg 9.6131183E-09 -5.1924082E-10 1,midg,midg; igrid,midg,midg 1.1702960E-08 2.7210254E-09 gauss-seidel spectral radius is 0.9874300 estimated iterations to convergence 73 setup time was (sec) 0.4200000 now iterating at: 14:20:22 rms-change max change #iterations 0.1240130 20.92626 at 10iterations 1.2655805E-02 1.884966 at 20iterations 1.2490767E-03 0.1994638 at 30iterations 1.2591928E-04 1.8007755E-02 at 40iterations 1.2635387E-05 1.9803047E-03 at 50iterations finished qdiffx linear iterations at : 14:20:29 total time elapsed so far: 2.810000 # loops : 50 mean,max change (kT/e) : 1.2635387E-05 1.9803047E-03 energy calculations done at 2.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.980000 DelPhi exited at 14:20:30 2.986u 0.146s 0:12.29 25.3% 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 Tue Nov 22 2011 at 14:20:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.930481 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): -6.129000 34.89800 ymin,ymax (A): -4.037000 49.53700 zmin,zma (A): -24.42000 30.90300 x,y,z range (A): 41.02700 53.57400 55.32300 scale (grids/A): 1.930481 object centre (A): 14.38450 22.75000 3.241500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 92.71629 97.72772 90.66953 assigned negative charge : -282.8263 centred at (gu) : 92.90800 97.99455 90.53452 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 60004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17080 grid for indexing accessible points = 1.400000 m= 22633 mr = 41877 m= 3396 mr = 17383 m= 174 mr = 2204 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1519 time to turn everything in is 0.4200000 number of dielectric boundary points 24680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14446 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) : 0.6434937 object centre at (A) : 14.38450 22.75000 3.241500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6762384E-02 2.2157136E-02 midg,1,midg; midg,igrid,midg 2.5991043E-02 4.1189217E-03 1,midg,midg; igrid,midg,midg 9.5081748E-03 1.0927732E-03 gauss-seidel spectral radius is 0.9985915 estimated iterations to convergence 211 setup time was (sec) 0.7000000 now iterating at: 14:20:37 rms-change max change #iterations 3.625140 156.9268 at 10iterations 1.687326 57.49670 at 20iterations 0.7778286 28.84407 at 30iterations 0.3621372 11.60905 at 40iterations 0.1671470 5.550146 at 50iterations 7.7345878E-02 2.820847 at 60iterations 3.5721846E-02 1.357869 at 70iterations 1.6485050E-02 0.5863647 at 80iterations 7.6242234E-03 0.2842827 at 90iterations 3.5268294E-03 0.1150990 at 100iterations 1.6370374E-03 5.5572510E-02 at 110iterations 7.5941609E-04 2.8266907E-02 at 120iterations finished qdiffx linear iterations at : 14:20:56 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 7.5941609E-04 2.8266907E-02 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 14:20:58 7.237u 0.191s 0:26.01 28.5% 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 Tue Nov 22 2011 at 14:21:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.895722 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): -6.129000 34.89800 ymin,ymax (A): -4.037000 49.53700 zmin,zma (A): -24.42000 30.90300 x,y,z range (A): 41.02700 53.57400 55.32300 scale (grids/A): 2.895722 object centre (A): 14.38450 22.75000 3.241500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 94.07442 101.5916 91.00430 assigned negative charge : -282.8263 centred at (gu) : 94.36209 101.9919 90.80185 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 138439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17080 grid for indexing accessible points = 1.400000 m= 72373 mr = 100746 m= 27280 mr = 60596 m= 6085 mr = 22786 m= 731 mr = 4675 m= 63 mr = 460 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 5028 time to turn everything in is 1.060000 number of dielectric boundary points 55687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 14640 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) : 1.930481 object centre at (A) : 14.38450 22.75000 3.241500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.077282 9.2221819E-02 midg,1,midg; midg,igrid,midg 0.2313229 -1.0465072E-02 1,midg,midg; igrid,midg,midg 5.7586394E-02 1.4000398E-02 gauss-seidel spectral radius is 0.9992334 estimated iterations to convergence 285 setup time was (sec) 1.330000 now iterating at: 14:21:07 rms-change max change #iterations 8.520507 580.5063 at 10iterations 4.888872 138.7812 at 20iterations 2.784099 74.02803 at 30iterations 1.582870 36.77238 at 40iterations 0.9010099 17.14851 at 50iterations 0.5120391 10.92872 at 60iterations 0.2901734 6.726455 at 70iterations 0.1645516 3.396498 at 80iterations 9.3536556E-02 1.844189 at 90iterations 5.3088654E-02 1.077652 at 100iterations 3.0073123E-02 0.5912764 at 110iterations 1.7099721E-02 0.3449218 at 120iterations 9.7108800E-03 0.2045417 at 130iterations 5.5030598E-03 0.1254368 at 140iterations 3.1255255E-03 7.6034546E-02 at 150iterations 1.7749220E-03 3.3519745E-02 at 160iterations 1.0062009E-03 2.2392273E-02 at 170iterations 5.7221996E-04 1.0698736E-02 at 180iterations finished qdiffx linear iterations at : 14:21:34 total time elapsed so far: 10.61000 # loops : 180 mean,max change (kT/e) : 5.7221996E-04 1.0698736E-02 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 14:21:36 10.796u 0.158s 0:36.89 29.6% 0+0k 0+0io 0pf+0w