Mon Oct 10 10:27:22 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 10:27:22 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! 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: 0.5519209 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): 16.30000 75.22100 ymin,ymax (A): -48.69900 6.186000 zmin,zma (A): 9.763000 74.26500 x,y,z range (A): 58.92100 54.88500 64.50200 scale (grids/A): 0.5519209 object centre (A): 45.76050 -21.25650 42.01400 number of atom coordinates read : 2986 total number of charged atoms : 2833 net assigned charge : 6.014024 assigned positive charge : 439.0257 centred at (gu) : 92.17325 90.25576 88.23827 assigned negative charge : -433.0122 centred at (gu) : 92.39946 90.35402 88.15309 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6262 nv = 96 ne = 84 npr = 56643 no. pairs analyzed = 56643 no. exposed pairs = 4649 no. arc points = 34198 no. surface atoms = 1531 nbur = 1455 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 = 1.568000 m= 269 mr = 2642 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3312 ## 394 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7912 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5923996E-10 7.8411255E-10 midg,1,midg; midg,igrid,midg 1.2239818E-09 -2.8191657E-10 1,midg,midg; igrid,midg,midg 1.3446695E-09 -2.3176117E-09 gauss-seidel spectral radius is 0.9830964 estimated iterations to convergence 63 setup time was (sec) 0.4200000 now iterating at: 10:27:22 rms-change max change #iterations 7.5472727E-02 11.89965 at 10iterations 5.1251994E-03 0.8566132 at 20iterations 3.4369080E-04 6.3548088E-02 at 30iterations 2.5322373E-05 4.9438477E-03 at 40iterations 2.2944598E-06 4.5204163E-04 at 50iterations finished qdiffx linear iterations at : 10:27:25 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.2944598E-06 4.5204163E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 10:27:26 3.452u 0.165s 0:03.93 91.8% 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 10:27:26 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! 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: 1.655763 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): 16.30000 75.22100 ymin,ymax (A): -48.69900 6.186000 zmin,zma (A): 9.763000 74.26500 x,y,z range (A): 58.92100 54.88500 64.50200 scale (grids/A): 1.655763 object centre (A): 45.76050 -21.25650 42.01400 number of atom coordinates read : 2986 total number of charged atoms : 2833 net assigned charge : 6.014024 assigned positive charge : 439.0257 centred at (gu) : 96.51921 90.76665 84.71441 assigned negative charge : -433.0122 centred at (gu) : 97.19798 91.06164 84.45898 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34198 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19831 mr = 39367 m= 2151 mr = 12154 m= 66 mr = 831 m= 0 mr = 1 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 258 time to turn everything in is 0.3600000 number of dielectric boundary points 36230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21782 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) : 0.5519209 object centre at (A) : 45.76050 -21.25650 42.01400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0713026E-03 2.2605563E-02 midg,1,midg; midg,igrid,midg 9.7391019E-03 8.0346260E-03 1,midg,midg; igrid,midg,midg 2.0932004E-02 -6.9878036E-03 gauss-seidel spectral radius is 0.9982645 estimated iterations to convergence 191 setup time was (sec) 0.5700000 now iterating at: 10:27:27 rms-change max change #iterations 3.397530 172.4343 at 10iterations 1.436752 63.16727 at 20iterations 0.6070308 24.44562 at 30iterations 0.2570224 10.00066 at 40iterations 0.1087557 4.100067 at 50iterations 4.6109814E-02 2.068043 at 60iterations 1.9505907E-02 0.7546465 at 70iterations 8.2223006E-03 0.3064880 at 80iterations 3.4837639E-03 0.1208992 at 90iterations 1.4758749E-03 5.5372238E-02 at 100iterations 6.2696182E-04 2.3524284E-02 at 110iterations 2.6634507E-04 1.0201931E-02 at 120iterations finished qdiffx linear iterations at : 10:27:34 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 2.6634507E-04 1.0201931E-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) 7.870000 DelPhi exited at 10:27:34 7.869u 0.199s 0:08.34 96.5% 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 Mon Oct 10 2011 at 10:27:34 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! 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: 2.483644 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): 16.30000 75.22100 ymin,ymax (A): -48.69900 6.186000 zmin,zma (A): 9.763000 74.26500 x,y,z range (A): 58.92100 54.88500 64.50200 scale (grids/A): 2.483644 object centre (A): 45.76050 -21.25650 42.01400 number of atom coordinates read : 2986 total number of charged atoms : 2833 net assigned charge : 6.014024 assigned positive charge : 439.0257 centred at (gu) : 99.77860 91.14989 82.07162 assigned negative charge : -433.0122 centred at (gu) : 100.7968 91.59223 81.68839 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 153711 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34198 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 66908 mr = 97917 m= 19593 mr = 48700 m= 3139 mr = 13350 m= 255 mr = 1709 m= 3 mr = 82 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 783 time to turn everything in is 0.8200000 number of dielectric boundary points 81851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 22644 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) : 1.655763 object centre at (A) : 45.76050 -21.25650 42.01400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2081604E-02 0.4910024 midg,1,midg; midg,igrid,midg 7.1630232E-02 0.1111800 1,midg,midg; igrid,midg,midg 0.3836879 -1.8418100E-02 gauss-seidel spectral radius is 0.9991775 estimated iterations to convergence 275 setup time was (sec) 1.050000 now iterating at: 10:27:35 rms-change max change #iterations 9.008281 289.6051 at 10iterations 5.225011 145.8561 at 20iterations 2.998078 78.28439 at 30iterations 1.705565 41.79338 at 40iterations 0.9656884 30.48034 at 50iterations 0.5440515 12.58874 at 60iterations 0.3060951 7.354658 at 70iterations 0.1721071 3.719139 at 80iterations 9.6301377E-02 2.154721 at 90iterations 5.4020017E-02 1.175854 at 100iterations 3.0109916E-02 0.6518347 at 110iterations 1.6875627E-02 0.3645020 at 120iterations 9.4166622E-03 0.1998439 at 130iterations 5.2404176E-03 0.1211472 at 140iterations 2.9253946E-03 5.8284760E-02 at 150iterations 1.6302413E-03 3.3461571E-02 at 160iterations 9.0911897E-04 2.1888733E-02 at 170iterations 5.0598284E-04 1.0608435E-02 at 180iterations finished qdiffx linear iterations at : 10:27:47 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 5.0598284E-04 1.0608435E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 10:27:47 12.744u 0.234s 0:13.27 97.7% 0+0k 0+0io 0pf+0w