Sat Oct 8 17:48:29 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 Sat Oct 8 2011 at 17:48:29 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3508 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5245090 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): -0.9960000 44.14800 ymin,ymax (A): -30.76300 25.73900 zmin,zma (A): 1.371000 69.24400 x,y,z range (A): 45.14400 56.50200 67.87300 scale (grids/A): 0.5245090 object centre (A): 21.57600 -2.512000 35.30750 number of atom coordinates read : 3508 total number of charged atoms : 3361 net assigned charge : -5.871982 assigned positive charge : 538.6441 centred at (gu) : 90.49943 91.98601 90.59736 assigned negative charge : -544.5178 centred at (gu) : 90.46146 91.94678 90.58382 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6067 nv = 96 ne = 84 npr = 71704 no. pairs analyzed = 71704 no. exposed pairs = 4207 no. arc points = 28897 no. surface atoms = 1430 nbur = 2078 mkacc time = 0.1600000 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 = 1.624000 m= 217 mr = 3260 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2873 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8126 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7504780E-10 -1.2554463E-10 midg,1,midg; midg,igrid,midg -1.7832347E-10 -2.5875220E-11 1,midg,midg; igrid,midg,midg -2.5523095E-10 -2.5440395E-11 gauss-seidel spectral radius is 0.9813090 estimated iterations to convergence 60 setup time was (sec) 0.6200000 now iterating at: 17:48:30 rms-change max change #iterations 6.7669168E-02 11.37563 at 10iterations 4.2142877E-03 0.6420650 at 20iterations 3.5957227E-04 7.0370674E-02 at 30iterations 6.9394402E-05 1.5172958E-02 at 40iterations 1.6946522E-05 3.7174225E-03 at 50iterations finished qdiffx linear iterations at : 17:48:33 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.6946522E-05 3.7174225E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 17:48:34 4.234u 0.234s 0:04.79 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 Sat Oct 8 2011 at 17:48:34 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3508 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.573527 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): -0.9960000 44.14800 ymin,ymax (A): -30.76300 25.73900 zmin,zma (A): 1.371000 69.24400 x,y,z range (A): 45.14400 56.50200 67.87300 scale (grids/A): 1.573527 object centre (A): 21.57600 -2.512000 35.30750 number of atom coordinates read : 3508 total number of charged atoms : 3361 net assigned charge : -5.871982 assigned positive charge : 538.6441 centred at (gu) : 91.49750 95.95663 91.79086 assigned negative charge : -544.5178 centred at (gu) : 91.38402 95.84001 91.75101 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28897 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20417 mr = 48234 m= 1794 mr = 14014 m= 32 mr = 828 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 224 time to turn everything in is 0.5100000 number of dielectric boundary points 28147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 438 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 25521 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) : 0.5245090 object centre at (A) : 21.57600 -2.512000 35.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7398133E-03 1.1920640E-02 midg,1,midg; midg,igrid,midg -7.5943526E-03 -1.1676555E-02 1,midg,midg; igrid,midg,midg -4.1124918E-03 3.6018711E-04 gauss-seidel spectral radius is 0.9980794 estimated iterations to convergence 181 setup time was (sec) 0.8700000 now iterating at: 17:48:35 rms-change max change #iterations 3.416552 141.3455 at 10iterations 1.387382 49.86700 at 20iterations 0.5633891 19.70194 at 30iterations 0.2304322 8.808001 at 40iterations 9.3943335E-02 3.244856 at 50iterations 3.8228057E-02 1.510872 at 60iterations 1.5592555E-02 0.5799179 at 70iterations 6.3905595E-03 0.2417033 at 80iterations 2.6349246E-03 8.7309837E-02 at 90iterations 1.1017971E-03 3.8402081E-02 at 100iterations 4.7924541E-04 2.1382093E-02 at 110iterations 2.2200440E-04 9.4077587E-03 at 120iterations finished qdiffx linear iterations at : 17:48:44 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 2.2200440E-04 9.4077587E-03 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 17:48:44 9.689u 0.286s 0:10.24 97.2% 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 Sat Oct 8 2011 at 17:48:44 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3508 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.360291 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): -0.9960000 44.14800 ymin,ymax (A): -30.76300 25.73900 zmin,zma (A): 1.371000 69.24400 x,y,z range (A): 45.14400 56.50200 67.87300 scale (grids/A): 2.360291 object centre (A): 21.57600 -2.512000 35.30750 number of atom coordinates read : 3508 total number of charged atoms : 3361 net assigned charge : -5.871982 assigned positive charge : 538.6441 centred at (gu) : 92.24596 98.93472 92.68626 assigned negative charge : -544.5178 centred at (gu) : 92.07605 98.75976 92.62648 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 160688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28897 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73186 mr = 117893 m= 18902 mr = 58333 m= 2506 mr = 14067 m= 110 mr = 1562 m= 3 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 713 time to turn everything in is 1.250000 number of dielectric boundary points 63511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 26833 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) : 1.573527 object centre at (A) : 21.57600 -2.512000 35.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2057350 0.1105587 midg,1,midg; midg,igrid,midg -0.1050212 -0.1520088 1,midg,midg; igrid,midg,midg -7.8115128E-02 2.5715781E-02 gauss-seidel spectral radius is 0.9991089 estimated iterations to convergence 265 setup time was (sec) 1.600000 now iterating at: 17:48:46 rms-change max change #iterations 9.001102 261.5837 at 10iterations 4.976927 121.2730 at 20iterations 2.741542 62.41217 at 30iterations 1.502773 28.40520 at 40iterations 0.8219301 16.60479 at 50iterations 0.4489576 9.085558 at 60iterations 0.2445909 5.243199 at 70iterations 0.1333284 3.064371 at 80iterations 7.2723515E-02 1.731756 at 90iterations 3.9567657E-02 0.7688522 at 100iterations 2.1490179E-02 0.4389353 at 110iterations 1.1716441E-02 0.2361565 at 120iterations 6.3970932E-03 0.1209745 at 130iterations 3.4831902E-03 6.5595627E-02 at 140iterations 1.9045143E-03 3.8803101E-02 at 150iterations 1.0434652E-03 2.1452427E-02 at 160iterations 5.7656551E-04 1.1247635E-02 at 170iterations 3.2293054E-04 8.3408356E-03 at 180iterations finished qdiffx linear iterations at : 17:49:00 total time elapsed so far: 15.17000 # loops : 180 mean,max change (kT/e) : 3.2293054E-04 8.3408356E-03 energy calculations done at 15.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.34000 DelPhi exited at 17:49:00 15.340u 0.273s 0:15.97 97.7% 0+0k 0+0io 0pf+0w