Sat Oct 8 17:08:08 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 17:08:08 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3565 !!! WARNING: SEP 41 has a net charge of -0.4750 !!! WARNING: ASL 227 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5164060 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): -4.804000 64.13400 ymin,ymax (A): 13.79700 76.61700 zmin,zma (A): -12.90600 34.69200 x,y,z range (A): 68.93800 62.82000 47.59800 scale (grids/A): 0.5164060 object centre (A): 29.66500 45.20700 10.89300 number of atom coordinates read : 3565 total number of charged atoms : 3416 net assigned charge : -7.074983 assigned positive charge : 543.6050 centred at (gu) : 90.14230 87.71564 89.35033 assigned negative charge : -550.6819 centred at (gu) : 90.13930 87.78128 89.36629 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5933 nv = 96 ne = 84 npr = 72993 no. pairs analyzed = 72993 no. exposed pairs = 4378 no. arc points = 30176 no. surface atoms = 1480 nbur = 2085 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 = 1.652000 m= 194 mr = 3099 m= 0 mr = 1 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2971 ## 462 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7974 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0926226E-10 -1.4742269E-10 midg,1,midg; midg,igrid,midg 6.5248112E-11 -1.6785499E-10 1,midg,midg; igrid,midg,midg -1.3600177E-10 -1.3035412E-10 gauss-seidel spectral radius is 0.9807270 estimated iterations to convergence 60 setup time was (sec) 0.5800000 now iterating at: 17:08:08 rms-change max change #iterations 6.2908739E-02 11.21354 at 10iterations 3.7280172E-03 0.6183958 at 20iterations 2.7691587E-04 4.5419693E-02 at 30iterations 5.2331976E-05 9.5033646E-03 at 40iterations 1.3792353E-05 2.4499893E-03 at 50iterations finished qdiffx linear iterations at : 17:08:11 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.3792353E-05 2.4499893E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 17:08:11 3.172u 0.142s 0:03.63 91.1% 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 17:08:11 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3565 !!! WARNING: SEP 41 has a net charge of -0.4750 !!! WARNING: ASL 227 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.549218 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): -4.804000 64.13400 ymin,ymax (A): 13.79700 76.61700 zmin,zma (A): -12.90600 34.69200 x,y,z range (A): 68.93800 62.82000 47.59800 scale (grids/A): 1.549218 object centre (A): 29.66500 45.20700 10.89300 number of atom coordinates read : 3565 total number of charged atoms : 3416 net assigned charge : -7.074983 assigned positive charge : 543.6050 centred at (gu) : 90.42580 83.14580 88.04995 assigned negative charge : -550.6819 centred at (gu) : 90.41756 83.34333 88.09830 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 66924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30176 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19684 mr = 46015 m= 1829 mr = 13248 m= 52 mr = 819 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.5000000 number of dielectric boundary points 28407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 451 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 25842 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) : 0.5164060 object centre at (A) : 29.66500 45.20700 10.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4271160E-04 -1.3374643E-03 midg,1,midg; midg,igrid,midg -1.4494075E-02 -1.4894419E-02 1,midg,midg; igrid,midg,midg 1.0618216E-02 -3.0322506E-03 gauss-seidel spectral radius is 0.9980200 estimated iterations to convergence 179 setup time was (sec) 0.7700000 now iterating at: 17:08:12 rms-change max change #iterations 3.318770 155.8598 at 10iterations 1.324455 55.11464 at 20iterations 0.5342835 18.53284 at 30iterations 0.2138853 8.620815 at 40iterations 8.5771337E-02 3.192276 at 50iterations 3.4589808E-02 1.445398 at 60iterations 1.3927902E-02 0.5211883 at 70iterations 5.5975490E-03 0.2308459 at 80iterations 2.2571699E-03 7.9472542E-02 at 90iterations 9.2187175E-04 3.2094955E-02 at 100iterations 3.8219060E-04 1.4259815E-02 at 110iterations 1.6421964E-04 5.8832169E-03 at 120iterations finished qdiffx linear iterations at : 17:08:18 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 1.6421964E-04 5.8832169E-03 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 17:08:19 6.880u 0.151s 0:07.34 95.7% 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 17:08:19 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3565 !!! WARNING: SEP 41 has a net charge of -0.4750 !!! WARNING: ASL 227 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.323827 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): -4.804000 64.13400 ymin,ymax (A): 13.79700 76.61700 zmin,zma (A): -12.90600 34.69200 x,y,z range (A): 68.93800 62.82000 47.59800 scale (grids/A): 2.323827 object centre (A): 29.66500 45.20700 10.89300 number of atom coordinates read : 3565 total number of charged atoms : 3416 net assigned charge : -7.074983 assigned positive charge : 543.6050 centred at (gu) : 90.63853 79.71841 87.07480 assigned negative charge : -550.6819 centred at (gu) : 90.62623 80.01482 87.14735 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 156076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30176 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 69960 mr = 113056 m= 18190 mr = 54895 m= 2660 mr = 13232 m= 146 mr = 1641 m= 0 mr = 43 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 520 time to turn everything in is 1.090000 number of dielectric boundary points 64165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 27265 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) : 1.549218 object centre at (A) : 29.66500 45.20700 10.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6370528E-03 -1.2443120E-02 midg,1,midg; midg,igrid,midg -0.3241058 -0.2841350 1,midg,midg; igrid,midg,midg 0.4782275 -4.6704732E-02 gauss-seidel spectral radius is 0.9990897 estimated iterations to convergence 262 setup time was (sec) 1.360000 now iterating at: 17:08:20 rms-change max change #iterations 8.913332 286.9583 at 10iterations 4.938173 136.3773 at 20iterations 2.724663 59.59589 at 30iterations 1.494077 33.23701 at 40iterations 0.8193226 25.48843 at 50iterations 0.4451640 11.73216 at 60iterations 0.2420029 5.420753 at 70iterations 0.1315970 2.899776 at 80iterations 7.1561411E-02 1.623016 at 90iterations 3.8748931E-02 0.8038254 at 100iterations 2.0990759E-02 0.4078054 at 110iterations 1.1378941E-02 0.2292066 at 120iterations 6.1469059E-03 0.1227837 at 130iterations 3.3400482E-03 7.7255249E-02 at 140iterations 1.8061774E-03 3.6386490E-02 at 150iterations 9.8129280E-04 2.0801544E-02 at 160iterations 5.3476274E-04 1.1282921E-02 at 170iterations 2.9286821E-04 5.7144761E-03 at 180iterations finished qdiffx linear iterations at : 17:08:30 total time elapsed so far: 10.72000 # loops : 180 mean,max change (kT/e) : 2.9286821E-04 5.7144761E-03 energy calculations done at 10.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.89000 DelPhi exited at 17:08:30 10.894u 0.183s 0:11.36 97.4% 0+0k 0+0io 0pf+0w