Sat Oct 15 12:41:15 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 12:41:15 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5134 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: 0.5190639 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): -32.10800 27.40000 ymin,ymax (A): -13.34600 55.23900 zmin,zma (A): -25.00200 37.85400 x,y,z range (A): 59.50800 68.58501 62.85600 scale (grids/A): 0.5190639 object centre (A): -2.354001 20.94650 6.426001 number of atom coordinates read : 5134 total number of charged atoms : 4969 net assigned charge : -1.999969 assigned positive charge : 763.6550 centred at (gu) : 87.94765 90.55981 89.95235 assigned negative charge : -765.6603 centred at (gu) : 87.87445 90.42355 89.95018 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8740 nv = 96 ne = 84 npr = 104057 no. pairs analyzed = 104057 no. exposed pairs = 6613 no. arc points = 46588 no. surface atoms = 2208 nbur = 2926 mkacc time = 0.2700000 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= 316 mr = 4364 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4514 ## 612 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 11732 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6336341E-11 -2.8337336E-11 midg,1,midg; midg,igrid,midg -5.0504501E-10 5.6970401E-10 1,midg,midg; igrid,midg,midg -5.6746757E-10 1.4533016E-10 gauss-seidel spectral radius is 0.9810452 estimated iterations to convergence 60 setup time was (sec) 0.8500000 now iterating at: 12:41:16 rms-change max change #iterations 7.6336160E-02 9.767727 at 10iterations 4.8039430E-03 0.7723484 at 20iterations 5.7561503E-04 0.1326866 at 30iterations 1.5984726E-04 3.9424896E-02 at 40iterations 5.1594718E-05 1.2252808E-02 at 50iterations finished qdiffx linear iterations at : 12:41:21 total time elapsed so far: 5.530000 # loops : 50 mean,max change (kT/e) : 5.1594718E-05 1.2252808E-02 energy calculations done at 5.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.700000 DelPhi exited at 12:41:21 5.705u 0.468s 0:06.56 93.9% 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 12:41:21 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5134 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: 1.557192 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): -32.10800 27.40000 ymin,ymax (A): -13.34600 55.23900 zmin,zma (A): -25.00200 37.85400 x,y,z range (A): 59.50800 68.58501 62.85600 scale (grids/A): 1.557192 object centre (A): -2.354001 20.94650 6.426001 number of atom coordinates read : 5134 total number of charged atoms : 4969 net assigned charge : -1.999969 assigned positive charge : 763.6550 centred at (gu) : 83.84109 91.67803 89.85561 assigned negative charge : -765.6603 centred at (gu) : 83.62283 91.27041 89.85036 start vw surface at 0.1900000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 98034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46588 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 28155 mr = 66096 m= 2352 mr = 18099 m= 50 mr = 895 m= 0 mr = 2 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 384 time to turn everything in is 0.8700000 number of dielectric boundary points 43499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 542 ## 6 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 37473 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) : 0.5190639 object centre at (A) : -2.354001 20.94650 6.426001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8891630E-03 3.9050099E-03 midg,1,midg; midg,igrid,midg 3.4065072E-03 1.2710302E-02 1,midg,midg; igrid,midg,midg -6.3370988E-03 -2.5825000E-03 gauss-seidel spectral radius is 0.9982188 estimated iterations to convergence 188 setup time was (sec) 1.230000 now iterating at: 12:41:23 rms-change max change #iterations 4.068584 145.2823 at 10iterations 1.706265 61.68047 at 20iterations 0.7169607 21.87794 at 30iterations 0.3009043 8.366966 at 40iterations 0.1272958 4.054293 at 50iterations 5.3466115E-02 1.825443 at 60iterations 2.2432411E-02 0.7276878 at 70iterations 9.5282784E-03 0.2843833 at 80iterations 4.0701418E-03 0.1312962 at 90iterations 1.7586461E-03 6.0398102E-02 at 100iterations 7.8593666E-04 2.7732849E-02 at 110iterations 3.8011002E-04 1.5029907E-02 at 120iterations finished qdiffx linear iterations at : 12:41:35 total time elapsed so far: 13.00000 # loops : 120 mean,max change (kT/e) : 3.8011002E-04 1.5029907E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 12:41:36 13.180u 0.512s 0:14.18 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 Sat Oct 15 2011 at 12:41:36 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5134 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: 2.335788 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): -32.10800 27.40000 ymin,ymax (A): -13.34600 55.23900 zmin,zma (A): -25.00200 37.85400 x,y,z range (A): 59.50800 68.58501 62.85600 scale (grids/A): 2.335788 object centre (A): -2.354001 20.94650 6.426001 number of atom coordinates read : 5134 total number of charged atoms : 4969 net assigned charge : -1.999969 assigned positive charge : 763.6550 centred at (gu) : 80.76126 92.51691 89.78284 assigned negative charge : -765.6603 centred at (gu) : 80.43434 91.90552 89.77524 start vw surface at 0.2000000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 228099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46588 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 100491 mr = 162747 m= 25015 mr = 76923 m= 3294 mr = 17472 m= 200 mr = 1861 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 1398 time to turn everything in is 2.080000 number of dielectric boundary points 98043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 39664 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) : 1.557192 object centre at (A) : -2.354001 20.94650 6.426001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1166356 3.6663283E-02 midg,1,midg; midg,igrid,midg 0.2611791 0.1273634 1,midg,midg; igrid,midg,midg -7.7656726E-03 -5.6087457E-02 gauss-seidel spectral radius is 0.9992114 estimated iterations to convergence 281 setup time was (sec) 2.500000 now iterating at: 12:41:39 rms-change max change #iterations 11.07503 338.9056 at 10iterations 6.507957 131.0294 at 20iterations 3.798641 80.47029 at 30iterations 2.201369 53.97677 at 40iterations 1.271381 24.99607 at 50iterations 0.7305554 14.58104 at 60iterations 0.4195468 7.981125 at 70iterations 0.2400870 4.624876 at 80iterations 0.1372520 2.704801 at 90iterations 7.8208558E-02 1.385563 at 100iterations 4.4598255E-02 0.9024687 at 110iterations 2.5425943E-02 0.4866300 at 120iterations 1.4444955E-02 0.3166885 at 130iterations 8.2136942E-03 0.1546326 at 140iterations 4.6878378E-03 7.9322815E-02 at 150iterations 2.6709964E-03 4.7073364E-02 at 160iterations 1.5302575E-03 3.2539368E-02 at 170iterations 8.8557205E-04 1.5949249E-02 at 180iterations finished qdiffx linear iterations at : 12:42:06 total time elapsed so far: 23.31000 # loops : 180 mean,max change (kT/e) : 8.8557205E-04 1.5949249E-02 energy calculations done at 23.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.49000 DelPhi exited at 12:42:07 23.499u 0.589s 0:31.52 76.3% 0+0k 0+0io 0pf+0w