Mon Oct 10 14:20:14 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 14:20:15 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 0.6223776 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): -7.881000 44.04600 ymin,ymax (A): 12.53100 69.73100 zmin,zma (A): 54.76600 106.6270 x,y,z range (A): 51.92700 57.20000 51.86100 scale (grids/A): 0.6223776 object centre (A): 18.08250 41.13100 80.69650 number of atom coordinates read : 2399 total number of charged atoms : 2240 net assigned charge : -3.999987 assigned positive charge : 352.0932 centred at (gu) : 90.01871 90.81667 90.05836 assigned negative charge : -356.0934 centred at (gu) : 89.78207 90.77215 90.03177 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6248 nv = 96 ne = 84 npr = 48886 no. pairs analyzed = 48886 no. exposed pairs = 3154 no. arc points = 22437 no. surface atoms = 1071 nbur = 1328 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3209 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2209 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7566 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1478541E-09 -1.7593573E-09 midg,1,midg; midg,igrid,midg -5.3579510E-09 -6.5302858E-10 1,midg,midg; igrid,midg,midg -1.9267169E-08 1.1635984E-08 gauss-seidel spectral radius is 0.9866177 estimated iterations to convergence 71 setup time was (sec) 0.8100000 now iterating at: 14:20:16 rms-change max change #iterations 0.1227386 17.88711 at 10iterations 1.1314665E-02 1.775577 at 20iterations 1.0521041E-03 0.1827698 at 30iterations 9.6798271E-05 1.4827728E-02 at 40iterations 9.1248612E-06 1.5411377E-03 at 50iterations finished qdiffx linear iterations at : 14:20:24 total time elapsed so far: 8.460000 # loops : 50 mean,max change (kT/e) : 9.1248612E-06 1.5411377E-03 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.630000 DelPhi exited at 14:20:24 8.636u 0.681s 0:09.64 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 14:20:24 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 1.867133 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): -7.881000 44.04600 ymin,ymax (A): 12.53100 69.73100 zmin,zma (A): 54.76600 106.6270 x,y,z range (A): 51.92700 57.20000 51.86100 scale (grids/A): 1.867133 object centre (A): 18.08250 41.13100 80.69650 number of atom coordinates read : 2399 total number of charged atoms : 2240 net assigned charge : -3.999987 assigned positive charge : 352.0932 centred at (gu) : 90.05568 92.44972 90.17480 assigned negative charge : -356.0934 centred at (gu) : 89.34602 92.31609 90.09498 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 67691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22437 grid for indexing accessible points = 1.400000 m= 22427 mr = 45409 m= 3005 mr = 15613 m= 151 mr = 1446 m= 6 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 30771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 17599 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) : 0.6223776 object centre at (A) : 18.08250 41.13100 80.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6125171E-02 -2.5795129E-04 midg,1,midg; midg,igrid,midg 2.6023218E-03 -3.0779312E-03 1,midg,midg; igrid,midg,midg -3.7779186E-02 7.0997658E-03 gauss-seidel spectral radius is 0.9985650 estimated iterations to convergence 209 setup time was (sec) 1.260000 now iterating at: 14:20:26 rms-change max change #iterations 3.879050 157.6994 at 10iterations 1.773559 61.48666 at 20iterations 0.8148134 27.28415 at 30iterations 0.3745671 13.01801 at 40iterations 0.1714224 6.177956 at 50iterations 7.8831725E-02 2.592813 at 60iterations 3.6146160E-02 1.168258 at 70iterations 1.6636642E-02 0.6146011 at 80iterations 7.6194801E-03 0.2547016 at 90iterations 3.4850636E-03 0.1189480 at 100iterations 1.6095077E-03 5.7712555E-02 at 110iterations 7.3858793E-04 2.3445129E-02 at 120iterations finished qdiffx linear iterations at : 14:20:45 total time elapsed so far: 20.42000 # loops : 120 mean,max change (kT/e) : 7.3858793E-04 2.3445129E-02 energy calculations done at 20.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.59000 DelPhi exited at 14:20:46 20.596u 0.751s 0:21.67 98.4% 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 14:20:46 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 2.800699 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): -7.881000 44.04600 ymin,ymax (A): 12.53100 69.73100 zmin,zma (A): 54.76600 106.6270 x,y,z range (A): 51.92700 57.20000 51.86100 scale (grids/A): 2.800699 object centre (A): 18.08250 41.13100 80.69650 number of atom coordinates read : 2399 total number of charged atoms : 2240 net assigned charge : -3.999987 assigned positive charge : 352.0932 centred at (gu) : 90.08353 93.67446 90.26194 assigned negative charge : -356.0934 centred at (gu) : 89.01905 93.47399 90.14240 start vw surface at 0.1200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 156797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22437 grid for indexing accessible points = 1.400000 m= 74738 mr = 110996 m= 24217 mr = 59391 m= 4794 mr = 18156 m= 571 mr = 3012 m= 33 mr = 270 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 69314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 17919 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) : 1.867133 object centre at (A) : 18.08250 41.13100 80.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2546920 -5.9957015E-03 midg,1,midg; midg,igrid,midg 0.1226968 -0.1015311 1,midg,midg; igrid,midg,midg -0.3895950 2.2370372E-02 gauss-seidel spectral radius is 0.9992434 estimated iterations to convergence 287 setup time was (sec) 2.340000 now iterating at: 14:20:49 rms-change max change #iterations 9.358424 477.4521 at 10iterations 5.480049 127.8699 at 20iterations 3.184707 71.74781 at 30iterations 1.837453 41.34369 at 40iterations 1.061151 23.73611 at 50iterations 0.6102631 13.06214 at 60iterations 0.3505001 7.045294 at 70iterations 0.2010556 4.303827 at 80iterations 0.1153151 2.294724 at 90iterations 6.5974265E-02 1.386013 at 100iterations 3.7717707E-02 0.8329554 at 110iterations 2.1549895E-02 0.4364748 at 120iterations 1.2341217E-02 0.2535343 at 130iterations 7.0307683E-03 0.1363564 at 140iterations 4.0215100E-03 8.0940247E-02 at 150iterations 2.2923772E-03 5.0880432E-02 at 160iterations 1.3105437E-03 3.1064987E-02 at 170iterations 7.4867124E-04 1.3900757E-02 at 180iterations finished qdiffx linear iterations at : 14:21:18 total time elapsed so far: 31.34000 # loops : 180 mean,max change (kT/e) : 7.4867124E-04 1.3900757E-02 energy calculations done at 31.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.52000 DelPhi exited at 14:21:19 31.528u 0.879s 0:32.87 98.5% 0+0k 0+0io 0pf+0w