Tue Oct 11 08:27:10 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 Tue Oct 11 2011 at 08:27:11 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5148600 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): -39.53900 29.60600 ymin,ymax (A): -20.79900 37.45900 zmin,zma (A): -53.58300 5.155000 x,y,z range (A): 69.14500 58.25800 58.73800 scale (grids/A): 0.5148600 object centre (A): -4.966501 8.330000 -24.21400 number of atom coordinates read : 3966 total number of charged atoms : 3768 net assigned charge : -6.499983 assigned positive charge : 601.5580 centred at (gu) : 88.83932 89.65309 90.37501 assigned negative charge : -608.0607 centred at (gu) : 88.74972 89.68353 90.27143 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6991 nv = 96 ne = 84 npr = 73856 no. pairs analyzed = 73856 no. exposed pairs = 5865 no. arc points = 42311 no. surface atoms = 1944 nbur = 2022 mkacc time = 0.1900000 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 = 1.652000 m= 260 mr = 3115 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4067 ## 620 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9198 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5067302E-10 1.7794383E-10 midg,1,midg; midg,igrid,midg -3.1628634E-11 -1.7382193E-10 1,midg,midg; igrid,midg,midg -4.7404719E-10 9.0645512E-11 gauss-seidel spectral radius is 0.9806731 estimated iterations to convergence 59 setup time was (sec) 0.6600000 now iterating at: 08:27:12 rms-change max change #iterations 6.1960369E-02 10.73496 at 10iterations 3.5841423E-03 0.6372681 at 20iterations 2.7980376E-04 5.1599026E-02 at 30iterations 5.4493292E-05 7.9822540E-03 at 40iterations 1.4657425E-05 2.0885468E-03 at 50iterations finished qdiffx linear iterations at : 08:27:16 total time elapsed so far: 4.660000 # loops : 50 mean,max change (kT/e) : 1.4657425E-05 2.0885468E-03 energy calculations done at 4.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.830000 DelPhi exited at 08:27:16 4.834u 0.377s 0:05.54 93.8% 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 Tue Oct 11 2011 at 08:27:16 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.544580 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): -39.53900 29.60600 ymin,ymax (A): -20.79900 37.45900 zmin,zma (A): -53.58300 5.155000 x,y,z range (A): 69.14500 58.25800 58.73800 scale (grids/A): 1.544580 object centre (A): -4.966501 8.330000 -24.21400 number of atom coordinates read : 3966 total number of charged atoms : 3768 net assigned charge : -6.499983 assigned positive charge : 601.5580 centred at (gu) : 86.51683 88.95843 91.12366 assigned negative charge : -608.0607 centred at (gu) : 86.24873 89.04999 90.81391 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42311 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20774 mr = 48248 m= 1622 mr = 12605 m= 33 mr = 486 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 448 time to turn everything in is 0.6300000 number of dielectric boundary points 38600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 567 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 28508 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) : 0.5148600 object centre at (A) : -4.966501 8.330000 -24.21400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6953606E-03 -9.7977521E-04 midg,1,midg; midg,igrid,midg -2.3422241E-03 -2.0699897E-03 1,midg,midg; igrid,midg,midg -5.2758069E-03 1.7846627E-02 gauss-seidel spectral radius is 0.9980995 estimated iterations to convergence 182 setup time was (sec) 0.9400000 now iterating at: 08:27:18 rms-change max change #iterations 3.469817 150.8892 at 10iterations 1.407634 57.98523 at 20iterations 0.5717372 22.24668 at 30iterations 0.2326887 8.928474 at 40iterations 9.4849564E-02 3.311584 at 50iterations 3.8487472E-02 1.427986 at 60iterations 1.5721064E-02 0.5473971 at 70iterations 6.4184535E-03 0.2199020 at 80iterations 2.6237946E-03 9.0442657E-02 at 90iterations 1.0846021E-03 3.7362099E-02 at 100iterations 4.4783071E-04 1.6376495E-02 at 110iterations 1.9039131E-04 6.9816113E-03 at 120iterations finished qdiffx linear iterations at : 08:27:28 total time elapsed so far: 11.82000 # loops : 120 mean,max change (kT/e) : 1.9039131E-04 6.9816113E-03 energy calculations done at 11.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 08:27:29 11.982u 0.450s 0:13.06 95.1% 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 Oct 11 2011 at 08:27:29 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.316870 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): -39.53900 29.60600 ymin,ymax (A): -20.79900 37.45900 zmin,zma (A): -53.58300 5.155000 x,y,z range (A): 69.14500 58.25800 58.73800 scale (grids/A): 2.316870 object centre (A): -4.966501 8.330000 -24.21400 number of atom coordinates read : 3966 total number of charged atoms : 3768 net assigned charge : -6.499983 assigned positive charge : 601.5580 centred at (gu) : 84.77487 88.43730 91.68526 assigned negative charge : -608.0607 centred at (gu) : 84.37308 88.57502 91.22086 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 180316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42311 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 74253 mr = 119939 m= 17866 mr = 54796 m= 2042 mr = 11775 m= 125 mr = 967 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 1494 time to turn everything in is 1.530000 number of dielectric boundary points 87103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 30078 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) : 1.544580 object centre at (A) : -4.966501 8.330000 -24.21400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2957106E-02 -3.5074074E-02 midg,1,midg; midg,igrid,midg -2.3142418E-02 -3.9879605E-02 1,midg,midg; igrid,midg,midg -1.3884314E-03 0.4898066 gauss-seidel spectral radius is 0.9991472 estimated iterations to convergence 270 setup time was (sec) 1.880000 now iterating at: 08:27:32 rms-change max change #iterations 9.599295 334.9568 at 10iterations 5.518031 141.8925 at 20iterations 3.134709 83.63124 at 30iterations 1.774435 37.27529 at 40iterations 0.9977779 22.94385 at 50iterations 0.5586841 11.75883 at 60iterations 0.3117775 6.854126 at 70iterations 0.1736031 3.527135 at 80iterations 9.6341312E-02 1.882897 at 90iterations 5.3608190E-02 1.215312 at 100iterations 2.9678455E-02 0.5727510 at 110iterations 1.6415959E-02 0.3565955 at 120iterations 9.0765012E-03 0.1809998 at 130iterations 5.0218152E-03 9.5859528E-02 at 140iterations 2.7780363E-03 6.0977936E-02 at 150iterations 1.5348963E-03 3.1845570E-02 at 160iterations 8.5072313E-04 1.6587257E-02 at 170iterations 4.6994339E-04 8.9569092E-03 at 180iterations finished qdiffx linear iterations at : 08:27:48 total time elapsed so far: 18.46000 # loops : 180 mean,max change (kT/e) : 4.6994339E-04 8.9569092E-03 energy calculations done at 18.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.61000 DelPhi exited at 08:27:49 18.619u 0.494s 0:19.54 97.7% 0+0k 0+0io 0pf+0w