Tue Nov 22 14:10:57 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 Tue Nov 22 2011 at 14:11:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 0.5720162 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): -26.21300 36.02300 ymin,ymax (A): -18.95800 20.45800 zmin,zma (A): -3.242000 38.73900 x,y,z range (A): 62.23600 39.41600 41.98100 scale (grids/A): 0.5720162 object centre (A): 4.905002 0.7500000 17.74850 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 287.8261 centred at (gu) : 90.00771 90.30283 90.47324 assigned negative charge : -284.8263 centred at (gu) : 90.03179 90.38675 90.58919 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4255 nv = 96 ne = 84 npr = 39955 no. pairs analyzed = 39955 no. exposed pairs = 2472 no. arc points = 17445 no. surface atoms = 835 nbur = 1125 mkacc time = 8.0000006E-02 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= 181 mr = 2282 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1819 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5384 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5547247E-09 -8.5871316E-10 midg,1,midg; midg,igrid,midg 1.3051324E-09 -4.4184179E-10 1,midg,midg; igrid,midg,midg 7.6363121E-10 2.4563451E-10 gauss-seidel spectral radius is 0.9841451 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 14:11:06 rms-change max change #iterations 7.0406526E-02 14.43678 at 10iterations 5.2619651E-03 1.033546 at 20iterations 4.0051795E-04 9.4207764E-02 at 30iterations 2.9630941E-05 6.0501099E-03 at 40iterations 2.1850265E-06 4.6348572E-04 at 50iterations finished qdiffx linear iterations at : 14:11:10 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 2.1850265E-06 4.6348572E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 14:11:13 3.155u 0.184s 0:10.70 31.1% 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 Tue Nov 22 2011 at 14:11:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 1.716049 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): -26.21300 36.02300 ymin,ymax (A): -18.95800 20.45800 zmin,zma (A): -3.242000 38.73900 x,y,z range (A): 62.23600 39.41600 41.98100 scale (grids/A): 1.716049 object centre (A): 4.905002 0.7500000 17.74850 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 287.8261 centred at (gu) : 90.02321 90.90852 91.41996 assigned negative charge : -284.8263 centred at (gu) : 90.09559 91.16045 91.76790 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 46542 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17445 grid for indexing accessible points = 1.400000 m= 15412 mr = 31513 m= 1605 mr = 11303 m= 55 mr = 890 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 763 time to turn everything in is 0.3400000 number of dielectric boundary points 19896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 14135 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) : 0.5720162 object centre at (A) : 4.905002 0.7500000 17.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5250893E-03 -4.5636175E-03 midg,1,midg; midg,igrid,midg 2.5234916E-03 -1.2465223E-03 1,midg,midg; igrid,midg,midg 3.0718114E-02 1.9267956E-02 gauss-seidel spectral radius is 0.9982410 estimated iterations to convergence 189 setup time was (sec) 0.6100000 now iterating at: 14:11:19 rms-change max change #iterations 2.868838 172.8484 at 10iterations 1.206568 53.44073 at 20iterations 0.5078400 22.03119 at 30iterations 0.2150087 8.854217 at 40iterations 9.0834975E-02 3.634819 at 50iterations 3.8339682E-02 1.560778 at 60iterations 1.6146213E-02 0.7420511 at 70iterations 6.8497732E-03 0.2778438 at 80iterations 2.8889871E-03 0.1337113 at 90iterations 1.2247959E-03 5.7235718E-02 at 100iterations 5.1469676E-04 2.1820068E-02 at 110iterations 2.1846393E-04 9.8037720E-03 at 120iterations finished qdiffx linear iterations at : 14:11:32 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 2.1846393E-04 9.8037720E-03 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 14:11:33 6.990u 0.328s 0:19.03 38.4% 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 Tue Nov 22 2011 at 14:11:34 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 2.574073 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): -26.21300 36.02300 ymin,ymax (A): -18.95800 20.45800 zmin,zma (A): -3.242000 38.73900 x,y,z range (A): 62.23600 39.41600 41.98100 scale (grids/A): 2.574073 object centre (A): 4.905002 0.7500000 17.74850 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 287.8261 centred at (gu) : 90.03486 91.36286 92.12994 assigned negative charge : -284.8263 centred at (gu) : 90.14339 91.74071 92.65191 start vw surface at 0.1100000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 107642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17445 grid for indexing accessible points = 1.400000 m= 52381 mr = 76334 m= 15904 mr = 42719 m= 2495 mr = 12757 m= 193 mr = 1751 m= 2 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 2481 time to turn everything in is 0.8000000 number of dielectric boundary points 44952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 14620 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) : 1.716049 object centre at (A) : 4.905002 0.7500000 17.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5765487E-02 -4.8685726E-02 midg,1,midg; midg,igrid,midg 2.1761945E-02 -1.6233891E-02 1,midg,midg; igrid,midg,midg 0.3892967 0.2238876 gauss-seidel spectral radius is 0.9991237 estimated iterations to convergence 267 setup time was (sec) 1.090000 now iterating at: 14:11:41 rms-change max change #iterations 7.116241 272.5468 at 10iterations 3.922410 128.6064 at 20iterations 2.150921 62.22295 at 30iterations 1.179190 29.98132 at 40iterations 0.6434228 15.97344 at 50iterations 0.3509245 8.079865 at 60iterations 0.1918909 4.675913 at 70iterations 0.1044685 2.486847 at 80iterations 5.6908149E-02 1.403049 at 90iterations 3.1072481E-02 0.7293320 at 100iterations 1.6936773E-02 0.4117889 at 110iterations 9.2249131E-03 0.2362863 at 120iterations 5.0202454E-03 0.1252165 at 130iterations 2.7472586E-03 7.3380142E-02 at 140iterations 1.4937511E-03 3.4642220E-02 at 150iterations 8.1562297E-04 1.9275665E-02 at 160iterations 4.4459518E-04 9.7255707E-03 at 170iterations 2.4248190E-04 5.8622360E-03 at 180iterations finished qdiffx linear iterations at : 14:12:06 total time elapsed so far: 10.40000 # loops : 180 mean,max change (kT/e) : 2.4248190E-04 5.8622360E-03 energy calculations done at 10.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.58000 DelPhi exited at 14:12:07 10.578u 0.228s 0:33.52 32.1% 0+0k 0+0io 0pf+0w