Wed Dec 28 11:02:10 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+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 Wed Dec 28 2011 at 11:02:10 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5741750 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): -35.07200 10.22800 ymin,ymax (A): 1.093000 41.03400 zmin,zma (A): -3.022000 58.98000 x,y,z range (A): 45.30000 39.94100 62.00200 scale (grids/A): 0.5741750 object centre (A): -12.42200 21.06350 27.97900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2259 centred at (gu) : 90.40096 89.58602 89.85200 assigned negative charge : -290.2262 centred at (gu) : 90.29604 89.72877 89.83941 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4255 nv = 96 ne = 84 npr = 40615 no. pairs analyzed = 40615 no. exposed pairs = 2455 no. arc points = 17258 no. surface atoms = 839 nbur = 1125 mkacc time = 0.1100000 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 = 1.512000 m= 184 mr = 2263 m= 0 mr = 8 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1755 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 5387 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0234645E-10 4.7719062E-10 midg,1,midg; midg,igrid,midg 2.2144675E-09 -1.2420508E-09 1,midg,midg; igrid,midg,midg -8.2706880E-10 1.7288765E-09 gauss-seidel spectral radius is 0.9842619 estimated iterations to convergence 65 setup time was (sec) 0.5400000 now iterating at: 11:02:11 rms-change max change #iterations 7.4102513E-02 13.12441 at 10iterations 5.6606312E-03 1.022858 at 20iterations 4.2802680E-04 7.4113846E-02 at 30iterations 3.1872311E-05 6.6890717E-03 at 40iterations 2.4387707E-06 4.2343140E-04 at 50iterations finished qdiffx linear iterations at : 11:02:16 total time elapsed so far: 4.890000 # loops : 50 mean,max change (kT/e) : 2.4387707E-06 4.2343140E-04 energy calculations done at 4.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.060000 DelPhi exited at 11:02:18 5.062u 0.436s 0:07.80 70.3% 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 Dec 28 2011 at 11:02:18 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.722525 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): -35.07200 10.22800 ymin,ymax (A): 1.093000 41.03400 zmin,zma (A): -3.022000 58.98000 x,y,z range (A): 45.30000 39.94100 62.00200 scale (grids/A): 1.722525 object centre (A): -12.42200 21.06350 27.97900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2259 centred at (gu) : 91.20274 88.75813 89.55576 assigned negative charge : -290.2262 centred at (gu) : 90.88847 89.18636 89.51827 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 46574 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17258 grid for indexing accessible points = 1.400000 m= 15067 mr = 31423 m= 1787 mr = 10963 m= 52 mr = 1013 m= 0 mr = 7 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 421 time to turn everything in is 0.4300000 number of dielectric boundary points 20074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14218 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) : 0.5741750 object centre at (A) : -12.42200 21.06350 27.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1718288E-02 2.0997617E-02 midg,1,midg; midg,igrid,midg 2.0183604E-03 -7.6639028E-03 1,midg,midg; igrid,midg,midg -3.0948804E-03 -8.6972001E-04 gauss-seidel spectral radius is 0.9982516 estimated iterations to convergence 190 setup time was (sec) 0.8500000 now iterating at: 11:02:19 rms-change max change #iterations 2.956308 154.3166 at 10iterations 1.240705 62.40382 at 20iterations 0.5279521 22.42198 at 30iterations 0.2239135 9.106374 at 40iterations 9.4787605E-02 4.313637 at 50iterations 4.0048573E-02 1.752231 at 60iterations 1.6999377E-02 0.6785874 at 70iterations 7.1899183E-03 0.3084545 at 80iterations 3.0384124E-03 0.1191254 at 90iterations 1.2923025E-03 5.0326616E-02 at 100iterations 5.4942211E-04 2.2573471E-02 at 110iterations 2.3219823E-04 1.1335373E-02 at 120iterations finished qdiffx linear iterations at : 11:02:33 total time elapsed so far: 14.51000 # loops : 120 mean,max change (kT/e) : 2.3219823E-04 1.1335373E-02 energy calculations done at 14.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.69000 DelPhi exited at 11:02:35 14.695u 0.626s 0:16.83 90.9% 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 Dec 28 2011 at 11:02:35 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.583787 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): -35.07200 10.22800 ymin,ymax (A): 1.093000 41.03400 zmin,zma (A): -3.022000 58.98000 x,y,z range (A): 45.30000 39.94100 62.00200 scale (grids/A): 2.583787 object centre (A): -12.42200 21.06350 27.97900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2259 centred at (gu) : 91.80414 88.13718 89.33367 assigned negative charge : -290.2262 centred at (gu) : 91.33273 88.77956 89.27759 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 107808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17258 grid for indexing accessible points = 1.400000 m= 50828 mr = 76280 m= 15889 mr = 41142 m= 2918 mr = 12809 m= 249 mr = 2093 m= 8 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1302 time to turn everything in is 0.9800000 number of dielectric boundary points 45246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 14646 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) : 1.722525 object centre at (A) : -12.42200 21.06350 27.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2458169 0.2198361 midg,1,midg; midg,igrid,midg -3.7748867E-03 -0.1085868 1,midg,midg; igrid,midg,midg -5.8850154E-02 -4.1602552E-02 gauss-seidel spectral radius is 0.9991238 estimated iterations to convergence 267 setup time was (sec) 1.380000 now iterating at: 11:02:36 rms-change max change #iterations 7.331117 268.5815 at 10iterations 4.054669 109.4943 at 20iterations 2.223465 57.30934 at 30iterations 1.217575 31.01202 at 40iterations 0.6676246 18.20958 at 50iterations 0.3650646 8.104099 at 60iterations 0.1987910 4.659463 at 70iterations 0.1083146 2.645478 at 80iterations 5.9187710E-02 1.327705 at 90iterations 3.2285947E-02 0.7914432 at 100iterations 1.7621621E-02 0.4392128 at 110iterations 9.5904497E-03 0.2131920 at 120iterations 5.2238889E-03 0.1313801 at 130iterations 2.8550634E-03 6.6273689E-02 at 140iterations 1.5575548E-03 3.5595655E-02 at 150iterations 8.5067609E-04 1.9875288E-02 at 160iterations 4.6357641E-04 1.0074139E-02 at 170iterations 2.5228079E-04 6.0462952E-03 at 180iterations finished qdiffx linear iterations at : 11:02:55 total time elapsed so far: 19.83000 # loops : 180 mean,max change (kT/e) : 2.5228079E-04 6.0462952E-03 energy calculations done at 19.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.00000 DelPhi exited at 11:02:56 20.002u 0.543s 0:21.28 96.5% 0+0k 0+0io 0pf+0w