Sun Oct 9 01:49:13 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 Sun Oct 9 2011 at 01:49:13 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 !!! WARNING: HIT 83 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5546812 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): -47.06100 7.337000 ymin,ymax (A): 175.8320 236.1300 zmin,zma (A): 78.97900 143.1600 x,y,z range (A): 54.39800 60.29799 64.18101 scale (grids/A): 0.5546812 object centre (A): -19.86200 205.9810 111.0695 number of atom coordinates read : 3275 total number of charged atoms : 3132 net assigned charge : 11.01404 assigned positive charge : 484.8786 centred at (gu) : 89.83726 90.23991 90.33877 assigned negative charge : -473.8663 centred at (gu) : 89.70115 90.17563 90.49342 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6819 nv = 96 ne = 84 npr = 62664 no. pairs analyzed = 62664 no. exposed pairs = 4584 no. arc points = 32491 no. surface atoms = 1505 nbur = 1770 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 = 1.540000 m= 305 mr = 3330 m= 0 mr = 9 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3400000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3256 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2562376E-09 -6.2535765E-10 midg,1,midg; midg,igrid,midg 3.1900813E-10 1.6860994E-09 1,midg,midg; igrid,midg,midg -4.0085860E-10 2.1869986E-09 gauss-seidel spectral radius is 0.9832762 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 01:49:14 rms-change max change #iterations 8.4240951E-02 12.67212 at 10iterations 5.8405786E-03 0.9026585 at 20iterations 4.0973502E-04 6.2801361E-02 at 30iterations 3.2598411E-05 4.3736696E-03 at 40iterations 3.9555630E-06 7.4386597E-04 at 50iterations finished qdiffx linear iterations at : 01:49:16 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 3.9555630E-06 7.4386597E-04 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 01:49:17 3.128u 0.131s 0:03.86 84.1% 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 Sun Oct 9 2011 at 01:49:17 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 !!! WARNING: HIT 83 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.664044 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): -47.06100 7.337000 ymin,ymax (A): 175.8320 236.1300 zmin,zma (A): 78.97900 143.1600 x,y,z range (A): 54.39800 60.29799 64.18101 scale (grids/A): 1.664044 object centre (A): -19.86200 205.9810 111.0695 number of atom coordinates read : 3275 total number of charged atoms : 3132 net assigned charge : 11.01404 assigned positive charge : 484.8786 centred at (gu) : 89.51100 90.71865 91.01522 assigned negative charge : -473.8663 centred at (gu) : 89.10316 90.52660 91.47998 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23260 mr = 49230 m= 2536 mr = 15352 m= 90 mr = 1310 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1612 time to turn everything in is 0.5100000 number of dielectric boundary points 35230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 335 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 24100 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) : 0.5546812 object centre at (A) : -19.86200 205.9810 111.0695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5189734E-03 -1.0677610E-02 midg,1,midg; midg,igrid,midg 1.0750445E-02 2.8200157E-02 1,midg,midg; igrid,midg,midg -2.6605870E-03 1.3900264E-02 gauss-seidel spectral radius is 0.9983084 estimated iterations to convergence 193 setup time was (sec) 0.7800000 now iterating at: 01:49:18 rms-change max change #iterations 3.597095 170.8057 at 10iterations 1.532161 52.25007 at 20iterations 0.6572581 22.84842 at 30iterations 0.2820720 9.774742 at 40iterations 0.1212177 4.258266 at 50iterations 5.1843245E-02 1.725427 at 60iterations 2.2151183E-02 0.8031859 at 70iterations 9.5534949E-03 0.3178110 at 80iterations 4.0780436E-03 0.1355371 at 90iterations 1.7489759E-03 6.5433979E-02 at 100iterations 7.5437338E-04 2.7204037E-02 at 110iterations 3.2438940E-04 1.1066437E-02 at 120iterations finished qdiffx linear iterations at : 01:49:24 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 3.2438940E-04 1.1066437E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 01:49:24 6.926u 0.173s 0:07.50 94.5% 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 Sun Oct 9 2011 at 01:49:24 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 !!! WARNING: HIT 83 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.496066 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): -47.06100 7.337000 ymin,ymax (A): 175.8320 236.1300 zmin,zma (A): 78.97900 143.1600 x,y,z range (A): 54.39800 60.29799 64.18101 scale (grids/A): 2.496066 object centre (A): -19.86200 205.9810 111.0695 number of atom coordinates read : 3275 total number of charged atoms : 3132 net assigned charge : 11.01404 assigned positive charge : 484.8786 centred at (gu) : 89.26646 91.07786 91.52262 assigned negative charge : -473.8663 centred at (gu) : 88.65453 90.78986 92.21980 start vw surface at 0.1900000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 174402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32491 grid for indexing accessible points = 1.400000 m= 79536 mr = 121029 m= 23105 mr = 61230 m= 4017 mr = 16928 m= 360 mr = 2687 m= 6 mr = 140 m= 3 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 5607 time to turn everything in is 1.250000 number of dielectric boundary points 79414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 25049 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) : 1.664044 object centre at (A) : -19.86200 205.9810 111.0695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2714929 -9.5078945E-02 midg,1,midg; midg,igrid,midg 0.1857336 0.4593570 1,midg,midg; igrid,midg,midg -7.2281003E-02 0.1236621 gauss-seidel spectral radius is 0.9991952 estimated iterations to convergence 278 setup time was (sec) 1.540000 now iterating at: 01:49:26 rms-change max change #iterations 9.313894 331.4144 at 10iterations 5.390875 125.5508 at 20iterations 3.079540 65.41642 at 30iterations 1.756265 36.28519 at 40iterations 0.9945794 20.69295 at 50iterations 0.5650410 10.69983 at 60iterations 0.3187470 6.281762 at 70iterations 0.1797834 3.672477 at 80iterations 0.1013095 2.049604 at 90iterations 5.6940317E-02 1.099178 at 100iterations 3.2034989E-02 0.6642861 at 110iterations 1.7983057E-02 0.3479085 at 120iterations 1.0105019E-02 0.1941600 at 130iterations 5.6717391E-03 0.1106071 at 140iterations 3.1810978E-03 6.3499451E-02 at 150iterations 1.7825071E-03 3.6633492E-02 at 160iterations 1.0005225E-03 1.9184113E-02 at 170iterations 5.6203711E-04 1.0742188E-02 at 180iterations finished qdiffx linear iterations at : 01:49:35 total time elapsed so far: 10.97000 # loops : 180 mean,max change (kT/e) : 5.6203711E-04 1.0742188E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.14000 DelPhi exited at 01:49:36 11.146u 0.188s 0:11.65 97.1% 0+0k 0+0io 0pf+0w