Sun Nov 13 23:53:29 PST 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 Sun Nov 13 2011 at 23:53:29 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6375815 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): 10.68700 66.52300 ymin,ymax (A): -32.53000 22.05600 zmin,zma (A): -51.73800 1.805000 x,y,z range (A): 55.83600 54.58600 53.54300 scale (grids/A): 0.6375815 object centre (A): 38.60500 -5.237000 -24.96650 number of atom coordinates read : 2740 total number of charged atoms : 2600 net assigned charge : 4.000014 assigned positive charge : 401.6136 centred at (gu) : 90.51202 88.07978 90.42598 assigned negative charge : -397.6145 centred at (gu) : 90.40711 87.99889 90.55798 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7746 nv = 96 ne = 84 npr = 53933 no. pairs analyzed = 53933 no. exposed pairs = 3679 no. arc points = 25754 no. surface atoms = 1238 nbur = 1502 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 4091 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2451 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9076 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8350425E-08 -1.0226183E-08 midg,1,midg; midg,igrid,midg -5.4881739E-09 9.6842374E-09 1,midg,midg; igrid,midg,midg -5.5034994E-09 1.9178961E-08 gauss-seidel spectral radius is 0.9872788 estimated iterations to convergence 72 setup time was (sec) 0.4300000 now iterating at: 23:53:30 rms-change max change #iterations 0.1459597 19.81511 at 10iterations 1.4413947E-02 2.003494 at 20iterations 1.4330528E-03 0.1922684 at 30iterations 1.5293869E-04 2.2380590E-02 at 40iterations 2.2371658E-05 3.2749176E-03 at 50iterations finished qdiffx linear iterations at : 23:53:33 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.2371658E-05 3.2749176E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 23:53:33 3.530u 0.192s 0:04.10 90.7% 0+0k 0+45896io 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 Nov 13 2011 at 23:53:33 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.912744 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): 10.68700 66.52300 ymin,ymax (A): -32.53000 22.05600 zmin,zma (A): -51.73800 1.805000 x,y,z range (A): 55.83600 54.58600 53.54300 scale (grids/A): 1.912744 object centre (A): 38.60500 -5.237000 -24.96650 number of atom coordinates read : 2740 total number of charged atoms : 2600 net assigned charge : 4.000014 assigned positive charge : 401.6136 centred at (gu) : 91.53540 84.23887 91.27705 assigned negative charge : -397.6145 centred at (gu) : 91.22093 83.99636 91.67366 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 83301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25754 grid for indexing accessible points = 1.400000 m= 29207 mr = 56537 m= 4147 mr = 20872 m= 209 mr = 2488 m= 5 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 774 time to turn everything in is 0.5200000 number of dielectric boundary points 36907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 20460 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) : 0.6375815 object centre at (A) : 38.60500 -5.237000 -24.96650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3376367E-02 -2.5766077E-02 midg,1,midg; midg,igrid,midg -8.3497558E-03 1.6518947E-02 1,midg,midg; igrid,midg,midg -1.5542869E-02 4.3273844E-02 gauss-seidel spectral radius is 0.9986701 estimated iterations to convergence 217 setup time was (sec) 0.7300000 now iterating at: 23:53:34 rms-change max change #iterations 4.335855 191.3625 at 10iterations 2.046702 76.66786 at 20iterations 0.9627628 30.78913 at 30iterations 0.4552050 14.75286 at 40iterations 0.2151834 6.837990 at 50iterations 0.1015667 3.491989 at 60iterations 4.7929175E-02 1.374250 at 70iterations 2.2693014E-02 0.6815987 at 80iterations 1.0712919E-02 0.3555603 at 90iterations 5.0589833E-03 0.1498260 at 100iterations 2.4075035E-03 7.2794437E-02 at 110iterations 1.1344173E-03 3.4596443E-02 at 120iterations finished qdiffx linear iterations at : 23:53:42 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 1.1344173E-03 3.4596443E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 23:53:42 8.186u 0.213s 0:08.68 96.6% 0+0k 0+45272io 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 Nov 13 2011 at 23:53:42 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.869117 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): 10.68700 66.52300 ymin,ymax (A): -32.53000 22.05600 zmin,zma (A): -51.73800 1.805000 x,y,z range (A): 55.83600 54.58600 53.54300 scale (grids/A): 2.869117 object centre (A): 38.60500 -5.237000 -24.96650 number of atom coordinates read : 2740 total number of charged atoms : 2600 net assigned charge : 4.000014 assigned positive charge : 401.6136 centred at (gu) : 92.30295 81.35820 91.91564 assigned negative charge : -397.6145 centred at (gu) : 91.83128 80.99454 92.51044 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 192740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25754 grid for indexing accessible points = 1.400000 m= 95269 mr = 137585 m= 33005 mr = 76478 m= 7291 mr = 25979 m= 851 mr = 5343 m= 49 mr = 491 m= 0 mr = 25 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 2821 time to turn everything in is 1.370000 number of dielectric boundary points 83304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 20793 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) : 1.912744 object centre at (A) : 38.60500 -5.237000 -24.96650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7124181 -0.2630038 midg,1,midg; midg,igrid,midg 8.2587115E-02 0.1530126 1,midg,midg; igrid,midg,midg -0.1034722 0.5849390 gauss-seidel spectral radius is 0.9992788 estimated iterations to convergence 294 setup time was (sec) 1.610000 now iterating at: 23:53:44 rms-change max change #iterations 10.21794 339.5391 at 10iterations 6.023063 123.6381 at 20iterations 3.527416 75.01369 at 30iterations 2.060161 44.71796 at 40iterations 1.203175 21.92210 at 50iterations 0.6980327 13.27772 at 60iterations 0.4053957 7.509947 at 70iterations 0.2351172 3.935498 at 80iterations 0.1364449 2.317593 at 90iterations 7.9073220E-02 1.420563 at 100iterations 4.5858216E-02 0.7846775 at 110iterations 2.6569791E-02 0.4828873 at 120iterations 1.5409423E-02 0.2538223 at 130iterations 8.9131771E-03 0.1569996 at 140iterations 5.1958947E-03 8.7970734E-02 at 150iterations 3.0198782E-03 5.3676605E-02 at 160iterations 1.7643145E-03 2.9788971E-02 at 170iterations 1.0408150E-03 2.0973206E-02 at 180iterations finished qdiffx linear iterations at : 23:53:55 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 1.0408150E-03 2.0973206E-02 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 23:53:56 13.436u 0.216s 0:13.95 97.7% 0+0k 0+45264io 0pf+0w