Sat Oct 15 12:40:54 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+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 Sat Oct 15 2011 at 12:40:54 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 = 6191 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: 0.4826857 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): 3.699000 77.45300 ymin,ymax (A): 22.67900 85.63500 zmin,zma (A): 6.164000 70.69800 x,y,z range (A): 73.75400 62.95600 64.53400 scale (grids/A): 0.4826857 object centre (A): 40.57600 54.15700 38.43100 number of atom coordinates read : 6191 total number of charged atoms : 6021 net assigned charge : -2.999997 assigned positive charge : 931.8912 centred at (gu) : 90.48548 88.73779 89.33636 assigned negative charge : -934.8997 centred at (gu) : 90.40517 88.73685 89.23139 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8870 nv = 96 ne = 84 npr = 125986 no. pairs analyzed = 125986 no. exposed pairs = 7727 no. arc points = 52652 no. surface atoms = 2593 nbur = 3598 mkacc time = 0.2100000 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 = 1.792000 m= 288 mr = 4564 m= 1 mr = 3 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 0.4100000 number of dielectric boundary points 4592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4932 ## 829 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 12069 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3640385E-10 7.3126429E-11 midg,1,midg; midg,igrid,midg -1.6755852E-11 -7.2100390E-12 1,midg,midg; igrid,midg,midg -7.7588123E-11 7.4801845E-11 gauss-seidel spectral radius is 0.9781559 estimated iterations to convergence 56 setup time was (sec) 0.5900000 now iterating at: 12:40:55 rms-change max change #iterations 5.7523366E-02 7.687523 at 10iterations 2.8480240E-03 0.5136633 at 20iterations 2.3087687E-04 4.0534973E-02 at 30iterations 5.2086856E-05 9.9987984E-03 at 40iterations 1.5307378E-05 2.7689934E-03 at 50iterations finished qdiffx linear iterations at : 12:40:58 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 1.5307378E-05 2.7689934E-03 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 12:40:59 3.715u 0.171s 0:04.18 92.8% 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 15 2011 at 12:40:59 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 = 6191 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: 1.448057 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): 3.699000 77.45300 ymin,ymax (A): 22.67900 85.63500 zmin,zma (A): 6.164000 70.69800 x,y,z range (A): 73.75400 62.95600 64.53400 scale (grids/A): 1.448057 object centre (A): 40.57600 54.15700 38.43100 number of atom coordinates read : 6191 total number of charged atoms : 6021 net assigned charge : -2.999997 assigned positive charge : 931.8912 centred at (gu) : 91.45476 86.21145 88.00726 assigned negative charge : -934.8997 centred at (gu) : 91.21479 86.21024 87.69400 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 101629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52652 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 26904 mr = 69581 m= 1816 mr = 17085 m= 33 mr = 652 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1135 time to turn everything in is 0.5000000 number of dielectric boundary points 43065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 834 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 44211 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) : 0.4826857 object centre at (A) : 40.57600 54.15700 38.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4659663E-03 3.7853962E-03 midg,1,midg; midg,igrid,midg -1.1828367E-03 -2.5501200E-03 1,midg,midg; igrid,midg,midg -7.4728988E-03 1.2950002E-02 gauss-seidel spectral radius is 0.9979795 estimated iterations to convergence 177 setup time was (sec) 0.7300000 now iterating at: 12:40:59 rms-change max change #iterations 3.842069 162.9607 at 10iterations 1.526578 53.43862 at 20iterations 0.6096371 19.68643 at 30iterations 0.2419652 7.568388 at 40iterations 9.6539721E-02 2.913883 at 50iterations 3.8500734E-02 1.325702 at 60iterations 1.5400538E-02 0.5255127 at 70iterations 6.1553568E-03 0.1899719 at 80iterations 2.4795460E-03 7.5740814E-02 at 90iterations 1.0106678E-03 3.2855988E-02 at 100iterations 4.2466319E-04 1.2890339E-02 at 110iterations 1.9106118E-04 7.0571899E-03 at 120iterations finished qdiffx linear iterations at : 12:41:07 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 1.9106118E-04 7.0571899E-03 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 12:41:07 8.157u 0.217s 0:08.69 96.2% 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 15 2011 at 12:41:07 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 = 6191 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.172086 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): 3.699000 77.45300 ymin,ymax (A): 22.67900 85.63500 zmin,zma (A): 6.164000 70.69800 x,y,z range (A): 73.75400 62.95600 64.53400 scale (grids/A): 2.172086 object centre (A): 40.57600 54.15700 38.43100 number of atom coordinates read : 6191 total number of charged atoms : 6021 net assigned charge : -2.999997 assigned positive charge : 931.8912 centred at (gu) : 92.18136 84.31655 87.01038 assigned negative charge : -934.8997 centred at (gu) : 91.82224 84.31520 86.54100 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 237820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52652 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 100552 mr = 172254 m= 21598 mr = 76667 m= 2314 mr = 14812 m= 77 mr = 1277 m= 0 mr = 3 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 3873 time to turn everything in is 1.190000 number of dielectric boundary points 97348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 47922 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) : 1.448057 object centre at (A) : 40.57600 54.15700 38.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1603626 1.8803062E-02 midg,1,midg; midg,igrid,midg -9.5476853E-03 -3.4414548E-02 1,midg,midg; igrid,midg,midg -1.6431799E-02 0.2052115 gauss-seidel spectral radius is 0.9991550 estimated iterations to convergence 272 setup time was (sec) 1.460000 now iterating at: 12:41:09 rms-change max change #iterations 10.90898 272.2388 at 10iterations 6.287030 149.2380 at 20iterations 3.589371 83.76289 at 30iterations 2.045479 50.21706 at 40iterations 1.158519 22.97601 at 50iterations 0.6542338 12.46168 at 60iterations 0.3678131 7.246573 at 70iterations 0.2073283 4.670609 at 80iterations 0.1158744 2.458015 at 90iterations 6.4992793E-02 1.397668 at 100iterations 3.6355764E-02 0.6648293 at 110iterations 2.0292796E-02 0.3550358 at 120iterations 1.1321650E-02 0.2134371 at 130iterations 6.3311253E-03 0.1247673 at 140iterations 3.5298404E-03 6.1134338E-02 at 150iterations 1.9700814E-03 3.5220623E-02 at 160iterations 1.1018075E-03 1.9192219E-02 at 170iterations 6.1778119E-04 1.1821747E-02 at 180iterations finished qdiffx linear iterations at : 12:41:21 total time elapsed so far: 13.59000 # loops : 180 mean,max change (kT/e) : 6.1778119E-04 1.1821747E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 12:41:22 13.706u 0.238s 0:14.42 96.6% 0+0k 0+0io 0pf+0w