Sun Oct 9 23:55:09 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 23:55:10 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 0.5633090 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): -28.14300 25.70600 ymin,ymax (A): 15.23700 72.65900 zmin,zma (A): -27.03600 36.16200 x,y,z range (A): 53.84900 57.42200 63.19800 scale (grids/A): 0.5633090 object centre (A): -1.218499 43.94800 4.563002 number of atom coordinates read : 2982 total number of charged atoms : 2839 net assigned charge : 2.525008 assigned positive charge : 458.6544 centred at (gu) : 89.97327 88.33099 89.81155 assigned negative charge : -456.1306 centred at (gu) : 89.94886 88.23173 89.82882 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6108 nv = 96 ne = 84 npr = 57777 no. pairs analyzed = 57777 no. exposed pairs = 4013 no. arc points = 29120 no. surface atoms = 1334 nbur = 1648 mkacc time = 8.9999996E-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 = 1.512000 m= 275 mr = 2966 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2300000 number of dielectric boundary points 3410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2946 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8014 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7121768E-10 1.0213570E-10 midg,1,midg; midg,igrid,midg -1.4499906E-09 1.0556659E-09 1,midg,midg; igrid,midg,midg 1.4776198E-11 6.3265077E-10 gauss-seidel spectral radius is 0.9837488 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 23:55:10 rms-change max change #iterations 8.6955287E-02 14.26951 at 10iterations 6.1355899E-03 0.9911652 at 20iterations 4.3563737E-04 8.6796761E-02 at 30iterations 3.2045638E-05 5.6705475E-03 at 40iterations 2.3565019E-06 3.6621094E-04 at 50iterations finished qdiffx linear iterations at : 23:55:13 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.3565019E-06 3.6621094E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 23:55:14 3.437u 0.211s 0:04.07 89.4% 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 Sun Oct 9 2011 at 23:55:14 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 1.689927 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): -28.14300 25.70600 ymin,ymax (A): 15.23700 72.65900 zmin,zma (A): -27.03600 36.16200 x,y,z range (A): 53.84900 57.42200 63.19800 scale (grids/A): 1.689927 object centre (A): -1.218499 43.94800 4.563002 number of atom coordinates read : 2982 total number of charged atoms : 2839 net assigned charge : 2.525008 assigned positive charge : 458.6544 centred at (gu) : 89.91882 84.99249 89.43375 assigned negative charge : -456.1306 centred at (gu) : 89.84636 84.69501 89.48646 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 67075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29120 grid for indexing accessible points = 1.400000 m= 20385 mr = 43221 m= 2316 mr = 13875 m= 64 mr = 1111 m= 0 mr = 6 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 694 time to turn everything in is 0.3500000 number of dielectric boundary points 31627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21870 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) : 0.5633090 object centre at (A) : -1.218499 43.94800 4.563002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5339148E-03 -4.5621316E-03 midg,1,midg; midg,igrid,midg -3.1977969E-03 1.5446635E-02 1,midg,midg; igrid,midg,midg 1.1480862E-03 7.4090168E-04 gauss-seidel spectral radius is 0.9983223 estimated iterations to convergence 194 setup time was (sec) 0.5700000 now iterating at: 23:55:14 rms-change max change #iterations 3.638016 176.8968 at 10iterations 1.551926 58.73241 at 20iterations 0.6680781 23.50288 at 30iterations 0.2872757 11.33394 at 40iterations 0.1232717 4.208302 at 50iterations 5.3056225E-02 1.806774 at 60iterations 2.2870407E-02 0.7951546 at 70iterations 9.8452205E-03 0.3603039 at 80iterations 4.2396532E-03 0.1408768 at 90iterations 1.8320020E-03 7.0458889E-02 at 100iterations 7.8624737E-04 2.8026581E-02 at 110iterations 3.3936580E-04 1.1618137E-02 at 120iterations finished qdiffx linear iterations at : 23:55:22 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 3.3936580E-04 1.1618137E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 23:55:22 7.806u 0.242s 0:08.52 94.3% 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 Sun Oct 9 2011 at 23:55:22 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 2.534890 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): -28.14300 25.70600 ymin,ymax (A): 15.23700 72.65900 zmin,zma (A): -27.03600 36.16200 x,y,z range (A): 53.84900 57.42200 63.19800 scale (grids/A): 2.534890 object centre (A): -1.218499 43.94800 4.563002 number of atom coordinates read : 2982 total number of charged atoms : 2839 net assigned charge : 2.525008 assigned positive charge : 458.6544 centred at (gu) : 89.87811 82.48851 89.15044 assigned negative charge : -456.1306 centred at (gu) : 89.76946 82.04260 89.22971 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 155609 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29120 grid for indexing accessible points = 1.400000 m= 69332 mr = 106209 m= 20408 mr = 53894 m= 3578 mr = 15248 m= 323 mr = 2360 m= 3 mr = 151 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 2351 time to turn everything in is 0.8300000 number of dielectric boundary points 71392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 22694 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) : 1.689927 object centre at (A) : -1.218499 43.94800 4.563002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3633503E-02 -4.2697690E-02 midg,1,midg; midg,igrid,midg 1.5159840E-02 0.2166623 1,midg,midg; igrid,midg,midg 2.9237226E-02 -1.0480316E-02 gauss-seidel spectral radius is 0.9991861 estimated iterations to convergence 277 setup time was (sec) 1.080000 now iterating at: 23:55:24 rms-change max change #iterations 9.251934 319.9694 at 10iterations 5.283431 139.0850 at 20iterations 2.995592 67.53860 at 30iterations 1.695154 38.46455 at 40iterations 0.9550995 23.75570 at 50iterations 0.5389346 12.36391 at 60iterations 0.3024928 6.322280 at 70iterations 0.1698533 3.403482 at 80iterations 9.5266975E-02 2.101056 at 90iterations 5.3265039E-02 1.049754 at 100iterations 2.9856611E-02 0.5635920 at 110iterations 1.6671322E-02 0.3462181 at 120iterations 9.3399873E-03 0.2229810 at 130iterations 5.2186102E-03 0.1137695 at 140iterations 2.9242716E-03 6.3232422E-02 at 150iterations 1.6326992E-03 3.0914307E-02 at 160iterations 9.1264077E-04 1.8310070E-02 at 170iterations 5.0973933E-04 1.0070801E-02 at 180iterations finished qdiffx linear iterations at : 23:55:35 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 5.0973933E-04 1.0070801E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 23:55:36 12.935u 0.207s 0:13.56 96.8% 0+0k 0+0io 0pf+0w