Mon Oct 10 17:07:14 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+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 17:07:14 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3776 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: 0.5502574 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 : 3776 total number of charged atoms : 3646 net assigned charge : 42.00005 assigned positive charge : 592.6970 centred at (gu) : 90.85184 89.16217 88.07178 assigned negative charge : -550.7004 centred at (gu) : 90.77749 89.28797 88.15697 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7592 nv = 96 ne = 84 npr = 65433 no. pairs analyzed = 65433 no. exposed pairs = 6051 no. arc points = 45756 no. surface atoms = 1989 nbur = 1787 mkacc time = 0.1800000 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= 302 mr = 2862 m= 0 mr = 5 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 5027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4610 ## 679 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9845 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1461494E-09 1.4141408E-09 midg,1,midg; midg,igrid,midg 5.1753801E-09 1.4925385E-09 1,midg,midg; igrid,midg,midg 1.8972641E-09 4.5967208E-09 gauss-seidel spectral radius is 0.9830653 estimated iterations to convergence 63 setup time was (sec) 0.6900000 now iterating at: 17:07:54 rms-change max change #iterations 8.3920188E-02 13.30878 at 10iterations 5.9269015E-03 0.9656696 at 20iterations 7.3099515E-04 7.9364777E-02 at 30iterations 1.8156877E-04 1.3921738E-02 at 40iterations 5.0913452E-05 3.7803650E-03 at 50iterations finished qdiffx linear iterations at : 17:07:58 total time elapsed so far: 5.250000 # loops : 50 mean,max change (kT/e) : 5.0913452E-05 3.7803650E-03 energy calculations done at 5.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.410000 DelPhi exited at 17:07:59 5.413u 0.521s 0:45.02 13.1% 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 Mon Oct 10 2011 at 17:07:59 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3776 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: 1.650772 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 : 3776 total number of charged atoms : 3646 net assigned charge : 42.00005 assigned positive charge : 592.6970 centred at (gu) : 92.55401 87.48462 84.21355 assigned negative charge : -550.7004 centred at (gu) : 92.33200 87.86357 84.47050 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45756 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21083 mr = 45331 m= 2079 mr = 11779 m= 57 mr = 734 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 46881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 675 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 27907 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 6.8122759E-02 1.5663305E-02 midg,1,midg; midg,igrid,midg 6.1830908E-02 2.6801096E-02 1,midg,midg; igrid,midg,midg 2.2293618E-02 8.4685639E-02 gauss-seidel spectral radius is 0.9983658 estimated iterations to convergence 196 setup time was (sec) 1.010000 now iterating at: 17:08:00 rms-change max change #iterations 3.893433 164.6907 at 10iterations 1.688115 69.57860 at 20iterations 0.7321966 23.23517 at 30iterations 0.3179731 11.86167 at 40iterations 0.1383570 4.900053 at 50iterations 6.0181435E-02 2.128004 at 60iterations 2.6172968E-02 0.9599915 at 70iterations 1.1417616E-02 0.3858283 at 80iterations 4.9799024E-03 0.1878662 at 90iterations 2.1951972E-03 7.1758270E-02 at 100iterations 9.7278564E-04 3.2176971E-02 at 110iterations 4.3557322E-04 1.3225555E-02 at 120iterations finished qdiffx linear iterations at : 17:08:11 total time elapsed so far: 11.69000 # loops : 120 mean,max change (kT/e) : 4.3557322E-04 1.3225555E-02 energy calculations done at 11.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 17:08:12 11.860u 0.474s 0:12.63 97.6% 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 Mon Oct 10 2011 at 17:08:12 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3776 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: 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 : 3776 total number of charged atoms : 3646 net assigned charge : 42.00005 assigned positive charge : 592.6970 centred at (gu) : 93.83064 86.22652 81.32005 assigned negative charge : -550.7004 centred at (gu) : 93.49798 86.79520 81.70568 start vw surface at 0.1400000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 188527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45756 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 73063 mr = 113501 m= 18665 mr = 50681 m= 2820 mr = 11820 m= 144 mr = 1494 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 105688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 29114 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 0.8906765 0.1833351 midg,1,midg; midg,igrid,midg 0.7387578 0.4285890 1,midg,midg; igrid,midg,midg 0.2490203 1.354936 gauss-seidel spectral radius is 0.9992588 estimated iterations to convergence 290 setup time was (sec) 2.030000 now iterating at: 17:08:14 rms-change max change #iterations 10.49281 317.9333 at 10iterations 6.349018 168.4288 at 20iterations 3.807648 87.97809 at 30iterations 2.255455 69.46107 at 40iterations 1.328480 33.26375 at 50iterations 0.7781543 20.20559 at 60iterations 0.4557973 11.59232 at 70iterations 0.2662686 5.889212 at 80iterations 0.1551117 3.334469 at 90iterations 8.9821413E-02 1.849201 at 100iterations 5.2222103E-02 1.357644 at 110iterations 3.0198345E-02 0.6393626 at 120iterations 1.7496509E-02 0.3724060 at 130iterations 1.0101137E-02 0.2201366 at 140iterations 5.8388882E-03 0.1194611 at 150iterations 3.3752057E-03 6.5513611E-02 at 160iterations 1.9479970E-03 4.4177055E-02 at 170iterations 1.1251903E-03 2.2247314E-02 at 180iterations finished qdiffx linear iterations at : 17:08:33 total time elapsed so far: 20.34000 # loops : 180 mean,max change (kT/e) : 1.1251903E-03 2.2247314E-02 energy calculations done at 20.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.55000 DelPhi exited at 17:08:33 20.552u 0.511s 0:21.36 98.5% 0+0k 0+0io 0pf+0w