Wed Feb 15 08:56:36 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:37 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3778 !!! WARNING: CA1 191 has a net charge of 2.0000 !!! WARNING: CA2 192 has a net charge of 2.0000 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: 0.5502574 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): -75.06100 -13.25200 ymin,ymax (A): 39.09400 98.36600 zmin,zma (A): 7.633000 72.33000 x,y,z range (A): 61.80900 59.27201 64.69700 scale (grids/A): 0.5502574 object centre (A): -44.15650 68.73000 39.98150 number of atom coordinates read : 3778 total number of charged atoms : 3648 net assigned charge : 46.00005 assigned positive charge : 596.6970 centred at (gu) : 90.88634 89.15891 88.07118 assigned negative charge : -550.7004 centred at (gu) : 90.77749 89.28797 88.15697 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7527 nv = 96 ne = 84 npr = 67154 no. pairs analyzed = 67154 no. exposed pairs = 6062 no. arc points = 45877 no. surface atoms = 1992 nbur = 1786 mkacc time = 0.1600000 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 = 1.568000 m= 298 mr = 2800 m= 0 mr = 5 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 5020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4627 ## 681 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9847 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6151609E-09 1.5933835E-09 midg,1,midg; midg,igrid,midg 5.5695635E-09 1.7015019E-09 1,midg,midg; igrid,midg,midg 1.8441644E-09 5.3962097E-09 gauss-seidel spectral radius is 0.9830637 estimated iterations to convergence 63 setup time was (sec) 0.6300000 now iterating at: 08:56:37 rms-change max change #iterations 8.7724954E-02 14.99280 at 10iterations 6.4848545E-03 1.140488 at 20iterations 8.8711013E-04 8.8733673E-02 at 30iterations 2.2460386E-04 1.6365051E-02 at 40iterations 6.2548948E-05 4.3888092E-03 at 50iterations finished qdiffx linear iterations at : 08:56:40 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 6.2548948E-05 4.3888092E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 08:56:41 3.529u 0.160s 0:04.33 84.9% 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 Wed Feb 15 2012 at 08:56:41 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3778 !!! WARNING: CA1 191 has a net charge of 2.0000 !!! WARNING: CA2 192 has a net charge of 2.0000 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: 1.650772 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): -75.06100 -13.25200 ymin,ymax (A): 39.09400 98.36600 zmin,zma (A): 7.633000 72.33000 x,y,z range (A): 61.80900 59.27201 64.69700 scale (grids/A): 1.650772 object centre (A): -44.15650 68.73000 39.98150 number of atom coordinates read : 3778 total number of charged atoms : 3648 net assigned charge : 46.00005 assigned positive charge : 596.6970 centred at (gu) : 92.65753 87.47486 84.21175 assigned negative charge : -550.7004 centred at (gu) : 92.33200 87.86357 84.47050 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 80625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45877 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20661 mr = 44407 m= 2061 mr = 11387 m= 54 mr = 714 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 46895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 676 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 27923 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) : 0.5502574 object centre at (A) : -44.15650 68.73000 39.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0684202E-02 1.7473383E-02 midg,1,midg; midg,igrid,midg 6.3498773E-02 2.8447459E-02 1,midg,midg; igrid,midg,midg 2.2804303E-02 9.2188478E-02 gauss-seidel spectral radius is 0.9983622 estimated iterations to convergence 196 setup time was (sec) 1.000000 now iterating at: 08:56:42 rms-change max change #iterations 3.923617 164.5474 at 10iterations 1.700599 69.45740 at 20iterations 0.7379634 24.30631 at 30iterations 0.3202078 11.93039 at 40iterations 0.1391279 4.884789 at 50iterations 6.0503170E-02 2.166203 at 60iterations 2.6307663E-02 1.033472 at 70iterations 1.1497042E-02 0.4064369 at 80iterations 5.0329058E-03 0.1987000 at 90iterations 2.2243774E-03 8.5470200E-02 at 100iterations 9.9039718E-04 3.0944824E-02 at 110iterations 4.4923378E-04 1.6387939E-02 at 120iterations finished qdiffx linear iterations at : 08:56:50 total time elapsed so far: 8.540000 # loops : 120 mean,max change (kT/e) : 4.4923378E-04 1.6387939E-02 energy calculations done at 8.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.710000 DelPhi exited at 08:56:51 8.716u 0.340s 0:09.66 93.6% 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 Wed Feb 15 2012 at 08:56:51 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3778 !!! WARNING: CA1 191 has a net charge of 2.0000 !!! WARNING: CA2 192 has a net charge of 2.0000 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: 2.476158 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): -75.06100 -13.25200 ymin,ymax (A): 39.09400 98.36600 zmin,zma (A): 7.633000 72.33000 x,y,z range (A): 61.80900 59.27201 64.69700 scale (grids/A): 2.476158 object centre (A): -44.15650 68.73000 39.98150 number of atom coordinates read : 3778 total number of charged atoms : 3648 net assigned charge : 46.00005 assigned positive charge : 596.6970 centred at (gu) : 93.98593 86.21188 81.31734 assigned negative charge : -550.7004 centred at (gu) : 93.49798 86.79520 81.70568 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 186534 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45877 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 71445 mr = 111443 m= 18288 mr = 49119 m= 2798 mr = 11459 m= 139 mr = 1462 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 105692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 29130 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) : 1.650772 object centre at (A) : -44.15650 68.73000 39.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9211863 0.2107639 midg,1,midg; midg,igrid,midg 0.7609982 0.4499669 1,midg,midg; igrid,midg,midg 0.2571281 1.470110 gauss-seidel spectral radius is 0.9992566 estimated iterations to convergence 289 setup time was (sec) 1.840000 now iterating at: 08:56:53 rms-change max change #iterations 10.59098 368.4922 at 10iterations 6.407123 167.5185 at 20iterations 3.835610 90.23473 at 30iterations 2.267679 57.67610 at 40iterations 1.334971 35.92850 at 50iterations 0.7818362 19.91583 at 60iterations 0.4570712 9.197222 at 70iterations 0.2668817 5.696476 at 80iterations 0.1552964 3.309700 at 90iterations 8.9986429E-02 1.978945 at 100iterations 5.2188739E-02 1.177937 at 110iterations 3.0165717E-02 0.6433969 at 120iterations 1.7467858E-02 0.3888083 at 130iterations 1.0067925E-02 0.2180424 at 140iterations 5.8171977E-03 0.1217642 at 150iterations 3.3613425E-03 6.9732666E-02 at 160iterations 1.9393527E-03 4.0145874E-02 at 170iterations 1.1195122E-03 2.0233154E-02 at 180iterations finished qdiffx linear iterations at : 08:57:05 total time elapsed so far: 13.55000 # loops : 180 mean,max change (kT/e) : 1.1195122E-03 2.0233154E-02 energy calculations done at 13.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.75000 DelPhi exited at 08:57:05 13.748u 0.272s 0:14.56 96.2% 0+0k 0+0io 0pf+0w