Thu Jan 26 15:34:29 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.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 Thu Jan 26 2012 at 15:34:29 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: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6013 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.8000 !!! WARNING: ZN1 1061 has a net charge of 1.4000 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: 0.3858326 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): -63.02200 -7.562000 ymin,ymax (A): -51.94300 40.32500 zmin,zma (A): -30.23400 38.61400 x,y,z range (A): 55.46000 92.26800 68.84800 scale (grids/A): 0.3858326 object centre (A): -35.29200 -5.808998 4.190000 number of atom coordinates read : 6013 total number of charged atoms : 5840 net assigned charge : -7.999987 assigned positive charge : 922.1339 centred at (gu) : 90.44546 90.78202 88.25109 assigned negative charge : -930.1422 centred at (gu) : 90.43200 90.79910 88.22947 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4993 nv = 96 ne = 84 npr = 123527 no. pairs analyzed = 123527 no. exposed pairs = 7204 no. arc points = 48028 no. surface atoms = 2420 nbur = 3593 mkacc time = 0.2000000 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 = 2.184000 m= 106 mr = 2453 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 2646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3528 ## 916 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6938 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4793549E-13 -6.6184694E-15 midg,1,midg; midg,igrid,midg -1.8572605E-14 -1.6010831E-13 1,midg,midg; igrid,midg,midg -9.6400210E-14 -3.9336173E-14 gauss-seidel spectral radius is 0.9659587 estimated iterations to convergence 46 setup time was (sec) 0.5900000 now iterating at: 15:34:30 rms-change max change #iterations 1.5891282E-02 3.008662 at 10iterations 1.4266034E-03 0.3496761 at 20iterations 4.7352110E-04 0.1139555 at 30iterations 1.6502019E-04 3.9169312E-02 at 40iterations 5.7860016E-05 1.3654709E-02 at 50iterations finished qdiffx linear iterations at : 15:34:33 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 5.7860016E-05 1.3654709E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 15:34:34 3.994u 0.242s 0:04.77 88.6% 0+0k 0+0io 4pf+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 Thu Jan 26 2012 at 15:34:34 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: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6013 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.8000 !!! WARNING: ZN1 1061 has a net charge of 1.4000 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: 1.157498 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): -63.02200 -7.562000 ymin,ymax (A): -51.94300 40.32500 zmin,zma (A): -30.23400 38.61400 x,y,z range (A): 55.46000 92.26800 68.84800 scale (grids/A): 1.157498 object centre (A): -35.29200 -5.808998 4.190000 number of atom coordinates read : 6013 total number of charged atoms : 5840 net assigned charge : -7.999987 assigned positive charge : 922.1339 centred at (gu) : 91.33473 92.34383 84.75095 assigned negative charge : -930.1422 centred at (gu) : 91.29562 92.39713 84.68810 start vw surface at 0.1600000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 61140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48028 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.044000 m= 11499 mr = 41566 m= 331 mr = 6393 m= 0 mr = 29 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 695 time to turn everything in is 0.3600000 number of dielectric boundary points 24982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1170 ## 63 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 37755 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) : 0.3858326 object centre at (A) : -35.29200 -5.808998 4.190000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6371630E-03 -9.4467384E-04 midg,1,midg; midg,igrid,midg -6.2171812E-03 -1.5826423E-03 1,midg,midg; igrid,midg,midg -8.5052328E-05 -9.1618131E-05 gauss-seidel spectral radius is 0.9965327 estimated iterations to convergence 136 setup time was (sec) 0.5800000 now iterating at: 15:34:35 rms-change max change #iterations 2.086329 108.9357 at 10iterations 0.6232064 26.85841 at 20iterations 0.1870699 8.229500 at 30iterations 5.6374803E-02 2.362366 at 40iterations 1.7302334E-02 0.8094676 at 50iterations 5.5971001E-03 0.2568512 at 60iterations 2.2275606E-03 9.6591949E-02 at 70iterations 1.2030733E-03 5.1254272E-02 at 80iterations 7.7610556E-04 3.2789230E-02 at 90iterations 5.2532961E-04 2.2134781E-02 at 100iterations 3.6059920E-04 1.5249252E-02 at 110iterations 2.4825102E-04 1.0511398E-02 at 120iterations finished qdiffx linear iterations at : 15:34:42 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 2.4825102E-04 1.0511398E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 15:34:43 8.018u 0.232s 0:08.86 93.0% 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 Thu Jan 26 2012 at 15:34:43 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: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6013 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.8000 !!! WARNING: ZN1 1061 has a net charge of 1.4000 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: 1.736247 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): -63.02200 -7.562000 ymin,ymax (A): -51.94300 40.32500 zmin,zma (A): -30.23400 38.61400 x,y,z range (A): 55.46000 92.26800 68.84800 scale (grids/A): 1.736247 object centre (A): -35.29200 -5.808998 4.190000 number of atom coordinates read : 6013 total number of charged atoms : 5840 net assigned charge : -7.999987 assigned positive charge : 922.1339 centred at (gu) : 92.00156 93.51527 82.12593 assigned negative charge : -930.1422 centred at (gu) : 91.94318 93.59592 82.03212 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 144822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48028 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.016000 m= 49225 mr = 104513 m= 6083 mr = 35508 m= 232 mr = 3615 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2161 time to turn everything in is 0.7500000 number of dielectric boundary points 56680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 438 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 45379 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) : 1.157498 object centre at (A) : -35.29200 -5.808998 4.190000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9199837E-02 -3.8849421E-02 midg,1,midg; midg,igrid,midg -0.2089002 -9.1989674E-02 1,midg,midg; igrid,midg,midg 2.1324130E-03 -2.4306374E-03 gauss-seidel spectral radius is 0.9986228 estimated iterations to convergence 214 setup time was (sec) 0.9800000 now iterating at: 15:34:44 rms-change max change #iterations 6.916496 220.7502 at 10iterations 3.355801 138.7039 at 20iterations 1.611964 52.66726 at 30iterations 0.7722703 24.11846 at 40iterations 0.3682567 9.209892 at 50iterations 0.1747335 4.781134 at 60iterations 8.2892485E-02 2.345486 at 70iterations 3.9377891E-02 0.9969854 at 80iterations 1.8622613E-02 0.4815216 at 90iterations 8.8399341E-03 0.2244650 at 100iterations 4.2094081E-03 0.1037064 at 110iterations 2.0376132E-03 5.1885605E-02 at 120iterations 1.0216871E-03 2.6298761E-02 at 130iterations 5.4910377E-04 1.4705658E-02 at 140iterations 3.2790221E-04 9.3712807E-03 at 150iterations 2.1748978E-04 5.7716370E-03 at 160iterations 1.5522000E-04 4.2221546E-03 at 170iterations 1.1508176E-04 3.0007362E-03 at 180iterations finished qdiffx linear iterations at : 15:34:56 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 1.1508176E-04 3.0007362E-03 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 15:34:56 12.692u 0.263s 0:13.48 96.0% 0+0k 0+0io 0pf+0w