Sun Oct 9 02:31:24 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 02:31:24 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3718 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: 0.5969648 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): -21.35100 37.50500 ymin,ymax (A): -25.51200 31.60600 zmin,zma (A): 23.94500 83.58000 x,y,z range (A): 58.85600 57.11800 59.63500 scale (grids/A): 0.5969648 object centre (A): 8.076999 3.047000 53.76250 number of atom coordinates read : 3718 total number of charged atoms : 3575 net assigned charge : -11.99997 assigned positive charge : 561.0649 centred at (gu) : 89.82820 89.49262 90.83374 assigned negative charge : -573.0678 centred at (gu) : 89.80248 89.52493 90.71418 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8865 nv = 96 ne = 84 npr = 76381 no. pairs analyzed = 76381 no. exposed pairs = 4388 no. arc points = 29990 no. surface atoms = 1491 nbur = 2227 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 = 1.456000 m= 400 mr = 5140 m= 0 mr = 41 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3065 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 11047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8222318E-09 1.3542004E-09 midg,1,midg; midg,igrid,midg -3.4948375E-09 -5.6258136E-09 1,midg,midg; igrid,midg,midg -6.2085337E-09 -3.3275458E-09 gauss-seidel spectral radius is 0.9855667 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 02:31:25 rms-change max change #iterations 0.1321077 15.61568 at 10iterations 1.2082070E-02 1.371504 at 20iterations 1.5600113E-03 0.1942139 at 30iterations 3.6063648E-04 4.6859741E-02 at 40iterations 1.0444268E-04 1.3904572E-02 at 50iterations finished qdiffx linear iterations at : 02:31:28 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.0444268E-04 1.3904572E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 02:31:28 3.517u 0.215s 0:04.01 92.7% 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 02:31:28 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3718 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.790895 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): -21.35100 37.50500 ymin,ymax (A): -25.51200 31.60600 zmin,zma (A): 23.94500 83.58000 x,y,z range (A): 58.85600 57.11800 59.63500 scale (grids/A): 1.790895 object centre (A): 8.076999 3.047000 53.76250 number of atom coordinates read : 3718 total number of charged atoms : 3575 net assigned charge : -11.99997 assigned positive charge : 561.0649 centred at (gu) : 89.48315 88.47655 92.50001 assigned negative charge : -573.0678 centred at (gu) : 89.40737 88.57471 92.14199 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 97351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29990 grid for indexing accessible points = 1.400000 m= 33711 mr = 69912 m= 4580 mr = 25179 m= 200 mr = 2888 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 708 time to turn everything in is 0.6500000 number of dielectric boundary points 37805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 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) : 0.5969648 object centre at (A) : 8.076999 3.047000 53.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1297067E-02 -1.7749816E-02 midg,1,midg; midg,igrid,midg -6.6442080E-03 -1.8725177E-02 1,midg,midg; igrid,midg,midg -4.1876845E-03 5.0862264E-03 gauss-seidel spectral radius is 0.9985553 estimated iterations to convergence 209 setup time was (sec) 0.9600000 now iterating at: 02:31:29 rms-change max change #iterations 4.658964 170.6983 at 10iterations 2.141577 63.73751 at 20iterations 0.9813501 28.50456 at 30iterations 0.4515751 13.94527 at 40iterations 0.2079557 5.675126 at 50iterations 9.5642902E-02 2.664398 at 60iterations 4.3935828E-02 1.164856 at 70iterations 2.0252950E-02 0.5628462 at 80iterations 9.3866680E-03 0.2827568 at 90iterations 4.3687006E-03 0.1184845 at 100iterations 2.0489118E-03 5.6756973E-02 at 110iterations 9.8478643E-04 2.8152466E-02 at 120iterations finished qdiffx linear iterations at : 02:31:37 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 9.8478643E-04 2.8152466E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.260000 DelPhi exited at 02:31:38 9.267u 0.253s 0:09.81 96.9% 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 Sun Oct 9 2011 at 02:31:38 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3718 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.686342 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): -21.35100 37.50500 ymin,ymax (A): -25.51200 31.60600 zmin,zma (A): 23.94500 83.58000 x,y,z range (A): 58.85600 57.11800 59.63500 scale (grids/A): 2.686342 object centre (A): 8.076999 3.047000 53.76250 number of atom coordinates read : 3718 total number of charged atoms : 3575 net assigned charge : -11.99997 assigned positive charge : 561.0649 centred at (gu) : 89.22437 87.71451 93.74973 assigned negative charge : -573.0678 centred at (gu) : 89.11089 87.86195 93.21296 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 226311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29990 grid for indexing accessible points = 1.400000 m= 112922 mr = 170200 m= 37634 mr = 93176 m= 7997 mr = 30395 m= 925 mr = 6134 m= 36 mr = 624 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2304 time to turn everything in is 1.640000 number of dielectric boundary points 85288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 28585 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) : 1.790895 object centre at (A) : 8.076999 3.047000 53.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3951512 -0.1047268 midg,1,midg; midg,igrid,midg -1.9861486E-02 -0.1321114 1,midg,midg; igrid,midg,midg -9.2134751E-02 0.1329505 gauss-seidel spectral radius is 0.9992706 estimated iterations to convergence 292 setup time was (sec) 1.980000 now iterating at: 02:31:40 rms-change max change #iterations 11.57585 346.4725 at 10iterations 6.914310 179.4469 at 20iterations 4.103391 102.4927 at 30iterations 2.415665 48.97081 at 40iterations 1.419267 30.37511 at 50iterations 0.8288599 18.17562 at 60iterations 0.4843026 9.337946 at 70iterations 0.2820546 6.051163 at 80iterations 0.1640798 3.701394 at 90iterations 9.5408157E-02 1.803371 at 100iterations 5.5343620E-02 0.9825058 at 110iterations 3.2077704E-02 0.5686193 at 120iterations 1.8606858E-02 0.3274288 at 130iterations 1.0792954E-02 0.1740184 at 140iterations 6.2422575E-03 0.1154480 at 150iterations 3.6088503E-03 5.9410095E-02 at 160iterations 2.0928856E-03 3.6474228E-02 at 170iterations 1.2124474E-03 1.9271851E-02 at 180iterations finished qdiffx linear iterations at : 02:31:51 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 1.2124474E-03 1.9271851E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 02:31:52 13.337u 0.253s 0:13.86 97.9% 0+0k 0+0io 0pf+0w