Mon Oct 10 17:01:54 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+sph.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 = amb.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 17:01:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2791 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6223558 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): -8.657001 48.54500 ymin,ymax (A): -8.356000 39.19100 zmin,zma (A): -0.3809999 55.21300 x,y,z range (A): 57.20200 47.54700 55.59400 scale (grids/A): 0.6223558 object centre (A): 19.94400 15.41750 27.41600 number of atom coordinates read : 2791 total number of charged atoms : 2650 net assigned charge : -3.499975 assigned positive charge : 419.1992 centred at (gu) : 88.93530 89.43030 89.12527 assigned negative charge : -422.7003 centred at (gu) : 88.83263 89.33245 89.07609 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7243 nv = 96 ne = 84 npr = 55678 no. pairs analyzed = 55678 no. exposed pairs = 3725 no. arc points = 26211 no. surface atoms = 1255 nbur = 1536 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3745 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3600000 number of dielectric boundary points 3833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2551 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8853 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.0637097E-09 7.5627687E-10 midg,1,midg; midg,igrid,midg -1.1886751E-08 4.0785095E-09 1,midg,midg; igrid,midg,midg -1.3758363E-08 3.9294639E-09 gauss-seidel spectral radius is 0.9866532 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 17:01:55 rms-change max change #iterations 0.1300917 19.22129 at 10iterations 1.2021024E-02 1.671589 at 20iterations 1.1205408E-03 0.1483994 at 30iterations 1.0169734E-04 1.5563250E-02 at 40iterations 9.6481226E-06 1.3327599E-03 at 50iterations finished qdiffx linear iterations at : 17:01:58 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 9.6481226E-06 1.3327599E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 17:02:01 4.175u 0.281s 0:06.70 66.4% 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 Mon Oct 10 2011 at 17:02:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2791 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.867067 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): -8.657001 48.54500 ymin,ymax (A): -8.356000 39.19100 zmin,zma (A): -0.3809999 55.21300 x,y,z range (A): 57.20200 47.54700 55.59400 scale (grids/A): 1.867067 object centre (A): 19.94400 15.41750 27.41600 number of atom coordinates read : 2791 total number of charged atoms : 2650 net assigned charge : -3.499975 assigned positive charge : 419.1992 centred at (gu) : 86.80522 88.29044 87.37504 assigned negative charge : -422.7003 centred at (gu) : 86.49766 87.99741 87.22780 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26211 grid for indexing accessible points = 1.400000 m= 26036 mr = 52642 m= 3546 mr = 18335 m= 150 mr = 1989 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1198 time to turn everything in is 0.7000000 number of dielectric boundary points 35434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 20780 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) : 0.6223558 object centre at (A) : 19.94400 15.41750 27.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4748282E-03 2.1058130E-04 midg,1,midg; midg,igrid,midg -1.8015213E-02 -3.3376331E-03 1,midg,midg; igrid,midg,midg -5.6977201E-02 2.9277546E-02 gauss-seidel spectral radius is 0.9986106 estimated iterations to convergence 213 setup time was (sec) 1.000000 now iterating at: 17:02:02 rms-change max change #iterations 4.240960 188.4782 at 10iterations 1.967384 74.81561 at 20iterations 0.9143658 31.80570 at 30iterations 0.4236279 14.62930 at 40iterations 0.1968751 5.981466 at 50iterations 9.1291457E-02 2.687096 at 60iterations 4.2524438E-02 1.301899 at 70iterations 1.9720536E-02 0.6258860 at 80iterations 9.1376770E-03 0.2938290 at 90iterations 4.2706914E-03 0.1401787 at 100iterations 1.9811029E-03 6.5077782E-02 at 110iterations 9.1865723E-04 2.8175354E-02 at 120iterations finished qdiffx linear iterations at : 17:02:11 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 9.1865723E-04 2.8175354E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.680000 DelPhi exited at 17:02:12 9.680u 0.280s 0:11.14 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 Mon Oct 10 2011 at 17:02:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2791 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.800601 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): -8.657001 48.54500 ymin,ymax (A): -8.356000 39.19100 zmin,zma (A): -0.3809999 55.21300 x,y,z range (A): 57.20200 47.54700 55.59400 scale (grids/A): 2.800601 object centre (A): 19.94400 15.41750 27.41600 number of atom coordinates read : 2791 total number of charged atoms : 2650 net assigned charge : -3.499975 assigned positive charge : 419.1992 centred at (gu) : 85.20750 87.43543 86.06242 assigned negative charge : -422.7003 centred at (gu) : 84.74635 86.99609 85.84173 start vw surface at 0.1500000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 182363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26211 grid for indexing accessible points = 1.400000 m= 86116 mr = 128698 m= 28732 mr = 68487 m= 6073 mr = 22304 m= 658 mr = 4259 m= 25 mr = 373 m= 0 mr = 14 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 3966 time to turn everything in is 1.740000 number of dielectric boundary points 79832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 21200 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) : 1.867067 object centre at (A) : 19.94400 15.41750 27.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1764482 -0.2625695 midg,1,midg; midg,igrid,midg -0.1349908 -7.3475234E-02 1,midg,midg; igrid,midg,midg -0.6565341 0.3992134 gauss-seidel spectral radius is 0.9992754 estimated iterations to convergence 293 setup time was (sec) 2.070000 now iterating at: 17:02:14 rms-change max change #iterations 10.26380 327.6324 at 10iterations 6.117379 176.8634 at 20iterations 3.612863 82.16138 at 30iterations 2.118021 49.51718 at 40iterations 1.238322 26.28594 at 50iterations 0.7213656 14.34326 at 60iterations 0.4193237 7.632064 at 70iterations 0.2440475 4.501442 at 80iterations 0.1414999 2.568226 at 90iterations 8.1859849E-02 1.704023 at 100iterations 4.7534782E-02 0.9206314 at 110iterations 2.7470164E-02 0.4917450 at 120iterations 1.5915673E-02 0.3001785 at 130iterations 9.2001222E-03 0.1682019 at 140iterations 5.3159189E-03 0.1141274 at 150iterations 3.0794558E-03 5.5088997E-02 at 160iterations 1.7827272E-03 3.1600296E-02 at 170iterations 1.0334227E-03 1.9426823E-02 at 180iterations finished qdiffx linear iterations at : 17:02:28 total time elapsed so far: 16.08000 # loops : 180 mean,max change (kT/e) : 1.0334227E-03 1.9426823E-02 energy calculations done at 16.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.25000 DelPhi exited at 17:02:30 16.252u 0.314s 0:18.41 89.9% 0+0k 0+0io 0pf+0w