Sat Oct 15 15:17:11 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 15 2011 at 15:17:11 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 = 3235 !!! WARNING: HIR 74 has a net charge of 0.5140 !!! WARNING: SEP 234 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5250040 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): 22.20800 78.58500 ymin,ymax (A): -24.74300 36.60700 zmin,zma (A): -13.41100 54.39800 x,y,z range (A): 56.37700 61.35000 67.80901 scale (grids/A): 0.5250040 object centre (A): 50.39650 5.931999 20.49350 number of atom coordinates read : 3235 total number of charged atoms : 3079 net assigned charge : 5.039021 assigned positive charge : 502.9853 centred at (gu) : 90.72425 88.27739 86.56271 assigned negative charge : -497.9468 centred at (gu) : 90.80149 88.51406 86.70354 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5598 nv = 96 ne = 84 npr = 63517 no. pairs analyzed = 63517 no. exposed pairs = 4304 no. arc points = 30797 no. surface atoms = 1434 nbur = 1801 mkacc time = 0.1400000 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= 232 mr = 2681 m= 0 mr = 3 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3140 ## 535 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7622 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3573027E-09 -1.4782027E-10 midg,1,midg; midg,igrid,midg 1.3233411E-09 -4.3810885E-10 1,midg,midg; igrid,midg,midg 2.9023003E-10 -1.8260438E-10 gauss-seidel spectral radius is 0.9813313 estimated iterations to convergence 60 setup time was (sec) 0.5500000 now iterating at: 15:17:11 rms-change max change #iterations 6.5160386E-02 13.18626 at 10iterations 3.9969138E-03 0.8041382 at 20iterations 2.6325515E-04 4.9552917E-02 at 30iterations 2.3685147E-05 4.3144226E-03 at 40iterations 3.5021133E-06 4.8828125E-04 at 50iterations finished qdiffx linear iterations at : 15:17:14 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 3.5021133E-06 4.8828125E-04 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 15:17:15 3.193u 0.145s 0:03.99 83.4% 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 Sat Oct 15 2011 at 15:17:15 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 = 3235 !!! WARNING: HIR 74 has a net charge of 0.5140 !!! WARNING: SEP 234 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.575012 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): 22.20800 78.58500 ymin,ymax (A): -24.74300 36.60700 zmin,zma (A): -13.41100 54.39800 x,y,z range (A): 56.37700 61.35000 67.80901 scale (grids/A): 1.575012 object centre (A): 50.39650 5.931999 20.49350 number of atom coordinates read : 3235 total number of charged atoms : 3079 net assigned charge : 5.039021 assigned positive charge : 502.9853 centred at (gu) : 92.17220 84.83144 79.68755 assigned negative charge : -497.9468 centred at (gu) : 92.40408 85.54161 80.11031 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 17237 mr = 40810 m= 1482 mr = 11031 m= 23 mr = 584 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.4500000 number of dielectric boundary points 29275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 438 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23227 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) : 0.5250040 object centre at (A) : 50.39650 5.931999 20.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1393429E-02 -3.8538945E-03 midg,1,midg; midg,igrid,midg 3.3512905E-02 -5.1413164E-03 1,midg,midg; igrid,midg,midg 1.9002124E-03 -1.9850573E-03 gauss-seidel spectral radius is 0.9980561 estimated iterations to convergence 180 setup time was (sec) 0.7300000 now iterating at: 15:17:16 rms-change max change #iterations 3.274731 141.1404 at 10iterations 1.315132 56.44891 at 20iterations 0.5291438 20.39082 at 30iterations 0.2140933 7.887474 at 40iterations 8.6482346E-02 3.522493 at 50iterations 3.4932412E-02 1.235199 at 60iterations 1.4103246E-02 0.5327778 at 70iterations 5.6976648E-03 0.2195206 at 80iterations 2.3113452E-03 9.2058182E-02 at 90iterations 9.3237311E-04 3.4722090E-02 at 100iterations 3.7928365E-04 1.4316559E-02 at 110iterations 1.5361716E-04 6.0520172E-03 at 120iterations finished qdiffx linear iterations at : 15:17:22 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 1.5361716E-04 6.0520172E-03 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 15:17:22 6.963u 0.151s 0:07.45 95.4% 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 Sat Oct 15 2011 at 15:17:22 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3235 !!! WARNING: HIR 74 has a net charge of 0.5140 !!! WARNING: SEP 234 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.362518 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): 22.20800 78.58500 ymin,ymax (A): -24.74300 36.60700 zmin,zma (A): -13.41100 54.39800 x,y,z range (A): 56.37700 61.35000 67.80901 scale (grids/A): 2.362518 object centre (A): 50.39650 5.931999 20.49350 number of atom coordinates read : 3235 total number of charged atoms : 3079 net assigned charge : 5.039021 assigned positive charge : 502.9853 centred at (gu) : 93.25826 82.24705 74.53123 assigned negative charge : -497.9468 centred at (gu) : 93.60606 83.31235 75.16531 start vw surface at 0.1700000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 146590 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 61901 mr = 100811 m= 15354 mr = 47191 m= 2101 mr = 10798 m= 100 mr = 1167 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 110 time to turn everything in is 1.090000 number of dielectric boundary points 66053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 24583 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) : 1.575012 object centre at (A) : 50.39650 5.931999 20.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3180345 -3.1934991E-02 midg,1,midg; midg,igrid,midg 0.5452332 -7.5446829E-02 1,midg,midg; igrid,midg,midg -5.8712978E-03 -3.4317315E-02 gauss-seidel spectral radius is 0.9990951 estimated iterations to convergence 263 setup time was (sec) 1.390000 now iterating at: 15:17:24 rms-change max change #iterations 8.682271 280.5642 at 10iterations 4.809551 135.8157 at 20iterations 2.650345 81.40791 at 30iterations 1.451147 46.47393 at 40iterations 0.7942171 19.37542 at 50iterations 0.4342245 10.04239 at 60iterations 0.2359011 5.398537 at 70iterations 0.1282190 3.041275 at 80iterations 6.9845356E-02 1.638268 at 90iterations 3.7942633E-02 0.8298321 at 100iterations 2.0568790E-02 0.4616203 at 110iterations 1.1158493E-02 0.2502441 at 120iterations 6.0657300E-03 0.1278114 at 130iterations 3.2881279E-03 8.1939220E-02 at 140iterations 1.7821573E-03 3.7055969E-02 at 150iterations 9.6977683E-04 2.2891998E-02 at 160iterations 5.2994385E-04 1.1571884E-02 at 170iterations 2.9070128E-04 6.3896179E-03 at 180iterations finished qdiffx linear iterations at : 15:17:35 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 2.9070128E-04 6.3896179E-03 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 15:17:35 12.403u 0.238s 0:12.91 97.8% 0+0k 0+0io 0pf+0w