Sat Oct 8 16:01:11 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 Sat Oct 8 2011 at 16:01:11 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.6611694 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): -2.217000 45.63000 ymin,ymax (A): -15.68200 29.40700 zmin,zma (A): -16.92300 36.92100 x,y,z range (A): 47.84700 45.08900 53.84400 scale (grids/A): 0.6611694 object centre (A): 21.70650 6.862500 9.998999 number of atom coordinates read : 2286 total number of charged atoms : 2226 net assigned charge : 3.806002 assigned positive charge : 343.5181 centred at (gu) : 90.76900 88.54427 90.08001 assigned negative charge : -339.7128 centred at (gu) : 90.82453 88.67770 90.13045 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6798 nv = 96 ne = 84 npr = 45185 no. pairs analyzed = 45185 no. exposed pairs = 3012 no. arc points = 20573 no. surface atoms = 1025 nbur = 1261 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 3707 m= 0 mr = 73 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2800000 number of dielectric boundary points 3442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2005 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8149 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8315879E-08 6.5951689E-10 midg,1,midg; midg,igrid,midg 4.4973664E-08 -1.0482751E-08 1,midg,midg; igrid,midg,midg 1.6668803E-08 -4.1266199E-10 gauss-seidel spectral radius is 0.9881191 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 16:01:12 rms-change max change #iterations 0.1545348 22.29389 at 10iterations 1.6476806E-02 2.653954 at 20iterations 1.8030691E-03 0.2334563 at 30iterations 2.1861178E-04 2.8955460E-02 at 40iterations 3.9753759E-05 6.4430237E-03 at 50iterations finished qdiffx linear iterations at : 16:01:16 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 3.9753759E-05 6.4430237E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 16:01:16 4.638u 0.393s 0:05.36 93.6% 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 Sat Oct 8 2011 at 16:01:16 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.983508 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): -2.217000 45.63000 ymin,ymax (A): -15.68200 29.40700 zmin,zma (A): -16.92300 36.92100 x,y,z range (A): 47.84700 45.08900 53.84400 scale (grids/A): 1.983508 object centre (A): 21.70650 6.862500 9.998999 number of atom coordinates read : 2286 total number of charged atoms : 2226 net assigned charge : 3.806002 assigned positive charge : 343.5181 centred at (gu) : 92.30663 85.63223 90.23986 assigned negative charge : -339.7128 centred at (gu) : 92.47348 86.03304 90.39133 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20573 grid for indexing accessible points = 1.400000 m= 27075 mr = 50816 m= 4929 mr = 19882 m= 388 mr = 3390 m= 4 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 325 time to turn everything in is 0.6300000 number of dielectric boundary points 31631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17592 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) : 0.6611694 object centre at (A) : 21.70650 6.862500 9.998999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9406166E-02 -2.1233900E-02 midg,1,midg; midg,igrid,midg 3.2861318E-02 -5.9139910E-03 1,midg,midg; igrid,midg,midg 8.3802724E-03 -4.3014314E-02 gauss-seidel spectral radius is 0.9987112 estimated iterations to convergence 221 setup time was (sec) 0.9300000 now iterating at: 16:01:18 rms-change max change #iterations 4.308619 191.6727 at 10iterations 2.055812 67.04524 at 20iterations 0.9835646 32.91996 at 30iterations 0.4717765 15.35297 at 40iterations 0.2263850 7.072364 at 50iterations 0.1083093 3.592216 at 60iterations 5.2139554E-02 1.553182 at 70iterations 2.4909412E-02 0.7872829 at 80iterations 1.1925794E-02 0.3715491 at 90iterations 5.7161739E-03 0.1807051 at 100iterations 2.7419038E-03 8.3806992E-02 at 110iterations 1.3219278E-03 4.2648315E-02 at 120iterations finished qdiffx linear iterations at : 16:01:28 total time elapsed so far: 11.16000 # loops : 120 mean,max change (kT/e) : 1.3219278E-03 4.2648315E-02 energy calculations done at 11.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 16:01:28 11.333u 0.407s 0:11.99 97.8% 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 Sat Oct 8 2011 at 16:01:29 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 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.975262 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): -2.217000 45.63000 ymin,ymax (A): -15.68200 29.40700 zmin,zma (A): -16.92300 36.92100 x,y,z range (A): 47.84700 45.08900 53.84400 scale (grids/A): 2.975262 object centre (A): 21.70650 6.862500 9.998999 number of atom coordinates read : 2286 total number of charged atoms : 2226 net assigned charge : 3.806002 assigned positive charge : 343.5181 centred at (gu) : 93.45987 83.44830 90.35963 assigned negative charge : -339.7128 centred at (gu) : 93.71019 84.04956 90.58693 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 169888 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20573 grid for indexing accessible points = 1.400000 m= 86058 mr = 123151 m= 33155 mr = 70132 m= 9208 mr = 26852 m= 1729 mr = 7265 m= 115 mr = 1294 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 1194 time to turn everything in is 1.600000 number of dielectric boundary points 71393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 17808 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) : 1.983508 object centre at (A) : 21.70650 6.862500 9.998999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1995220 -0.2652809 midg,1,midg; midg,igrid,midg 0.2594447 -7.5912364E-02 1,midg,midg; igrid,midg,midg 7.3364235E-02 -0.6632714 gauss-seidel spectral radius is 0.9992808 estimated iterations to convergence 294 setup time was (sec) 1.930000 now iterating at: 16:01:31 rms-change max change #iterations 9.899415 473.6122 at 10iterations 5.823886 134.1982 at 20iterations 3.419642 71.99568 at 30iterations 2.003106 38.75088 at 40iterations 1.170263 26.71961 at 50iterations 0.6836801 15.05556 at 60iterations 0.3989216 7.412804 at 70iterations 0.2320403 4.519964 at 80iterations 0.1347414 2.540470 at 90iterations 7.8384303E-02 1.617072 at 100iterations 4.5454863E-02 0.8668547 at 110iterations 2.6435666E-02 0.4749146 at 120iterations 1.5323040E-02 0.2746468 at 130iterations 8.8782981E-03 0.1619873 at 140iterations 5.1662093E-03 9.2651367E-02 at 150iterations 3.0004927E-03 5.3638458E-02 at 160iterations 1.7409435E-03 3.3745766E-02 at 170iterations 1.0154473E-03 1.8534660E-02 at 180iterations finished qdiffx linear iterations at : 16:01:48 total time elapsed so far: 18.71000 # loops : 180 mean,max change (kT/e) : 1.0154473E-03 1.8534660E-02 energy calculations done at 18.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.87000 DelPhi exited at 16:01:48 18.879u 0.449s 0:19.59 98.5% 0+0k 0+0io 0pf+0w