Sun Oct 9 09:59:47 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 Sun Oct 9 2011 at 09:59:47 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 !!! WARNING: HIR 211 has a net charge of 0.5140 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: 0.5847281 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): -18.34300 42.54000 ymin,ymax (A): -26.24300 22.25300 zmin,zma (A): -29.24000 27.35600 x,y,z range (A): 60.88300 48.49600 56.59600 scale (grids/A): 0.5847281 object centre (A): 12.09850 -1.995000 -0.9420004 number of atom coordinates read : 2778 total number of charged atoms : 2701 net assigned charge : 2.514014 assigned positive charge : 416.6292 centred at (gu) : 88.60597 90.78810 91.57349 assigned negative charge : -414.1169 centred at (gu) : 88.58002 90.70696 91.52644 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6589 nv = 96 ne = 84 npr = 52765 no. pairs analyzed = 52765 no. exposed pairs = 3935 no. arc points = 27775 no. surface atoms = 1319 nbur = 1459 mkacc time = 9.0000004E-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 = 1.484000 m= 335 mr = 3248 m= 1 mr = 13 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 0.2000000 number of dielectric boundary points 3664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2773 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8237 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4481251E-10 2.5042521E-09 midg,1,midg; midg,igrid,midg -1.1041086E-09 3.0462346E-09 1,midg,midg; igrid,midg,midg -1.9766321E-11 8.9661417E-10 gauss-seidel spectral radius is 0.9849004 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 09:59:48 rms-change max change #iterations 9.8751836E-02 16.70133 at 10iterations 7.9579670E-03 1.133712 at 20iterations 9.2046062E-04 0.1848164 at 30iterations 2.1147344E-04 4.1149139E-02 at 40iterations 6.1118626E-05 1.2048721E-02 at 50iterations finished qdiffx linear iterations at : 09:59:50 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 6.1118626E-05 1.2048721E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 09:59:51 3.363u 0.178s 0:03.81 92.6% 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 Sun Oct 9 2011 at 09:59:51 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 !!! WARNING: HIR 211 has a net charge of 0.5140 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: 1.754184 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): -18.34300 42.54000 ymin,ymax (A): -26.24300 22.25300 zmin,zma (A): -29.24000 27.35600 x,y,z range (A): 60.88300 48.49600 56.59600 scale (grids/A): 1.754184 object centre (A): 12.09850 -1.995000 -0.9420004 number of atom coordinates read : 2778 total number of charged atoms : 2701 net assigned charge : 2.514014 assigned positive charge : 416.6292 centred at (gu) : 85.81713 92.36372 94.71944 assigned negative charge : -414.1169 centred at (gu) : 85.74014 92.12076 94.57932 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27775 grid for indexing accessible points = 1.400000 m= 23921 mr = 47239 m= 3470 mr = 16118 m= 171 mr = 1907 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 34040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 21040 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) : 0.5847281 object centre at (A) : 12.09850 -1.995000 -0.9420004 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3095539E-02 1.3723355E-02 midg,1,midg; midg,igrid,midg 6.3076434E-03 2.4079081E-02 1,midg,midg; igrid,midg,midg -7.7962894E-03 -2.5994249E-03 gauss-seidel spectral radius is 0.9984364 estimated iterations to convergence 201 setup time was (sec) 0.5600000 now iterating at: 09:59:52 rms-change max change #iterations 3.710525 142.3929 at 10iterations 1.638592 57.69141 at 20iterations 0.7258568 27.05514 at 30iterations 0.3232765 10.63512 at 40iterations 0.1429026 5.349030 at 50iterations 6.3503094E-02 2.128862 at 60iterations 2.8158214E-02 0.9701824 at 70iterations 1.2533313E-02 0.4525909 at 80iterations 5.6084911E-03 0.1964417 at 90iterations 2.5398710E-03 9.0117455E-02 at 100iterations 1.1680791E-03 4.0849686E-02 at 110iterations 5.5789907E-04 2.3614883E-02 at 120iterations finished qdiffx linear iterations at : 09:59:59 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 5.5789907E-04 2.3614883E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 09:59:59 7.696u 0.193s 0:08.17 96.4% 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 Sun Oct 9 2011 at 09:59:59 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 !!! WARNING: HIR 211 has a net charge of 0.5140 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: 2.631276 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): -18.34300 42.54000 ymin,ymax (A): -26.24300 22.25300 zmin,zma (A): -29.24000 27.35600 x,y,z range (A): 60.88300 48.49600 56.59600 scale (grids/A): 2.631276 object centre (A): 12.09850 -1.995000 -0.9420004 number of atom coordinates read : 2778 total number of charged atoms : 2701 net assigned charge : 2.514014 assigned positive charge : 416.6292 centred at (gu) : 83.72545 93.54520 97.07897 assigned negative charge : -414.1169 centred at (gu) : 83.61023 93.18112 96.86900 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 166264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27775 grid for indexing accessible points = 1.400000 m= 78684 mr = 116149 m= 26372 mr = 60914 m= 5932 mr = 19668 m= 706 mr = 4018 m= 19 mr = 403 m= 0 mr = 2 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 76823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 21601 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) : 1.754184 object centre at (A) : 12.09850 -1.995000 -0.9420004 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1194141 0.1649631 midg,1,midg; midg,igrid,midg 0.1178550 0.3052875 1,midg,midg; igrid,midg,midg -8.1527516E-02 3.9557558E-02 gauss-seidel spectral radius is 0.9992163 estimated iterations to convergence 282 setup time was (sec) 1.110000 now iterating at: 10:00:00 rms-change max change #iterations 9.392112 292.2755 at 10iterations 5.493812 137.1360 at 20iterations 3.182378 89.79301 at 30iterations 1.832676 42.88335 at 40iterations 1.052162 23.09749 at 50iterations 0.6016745 14.11358 at 60iterations 0.3431886 6.637177 at 70iterations 0.1958916 3.755217 at 80iterations 0.1111587 2.129551 at 90iterations 6.3308001E-02 1.495964 at 100iterations 3.5875726E-02 0.6920662 at 110iterations 2.0390505E-02 0.4090385 at 120iterations 1.1545661E-02 0.2645874 at 130iterations 6.5480126E-03 0.1330986 at 140iterations 3.7231729E-03 6.7405701E-02 at 150iterations 2.1155684E-03 4.2381287E-02 at 160iterations 1.2080844E-03 2.2438049E-02 at 170iterations 6.9588295E-04 1.4844894E-02 at 180iterations finished qdiffx linear iterations at : 10:00:12 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 6.9588295E-04 1.4844894E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 10:00:12 12.440u 0.195s 0:12.90 97.9% 0+0k 0+0io 0pf+0w