Tue Nov 22 14:10:02 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 14:10:06 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6396205 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): -5.277000 34.71600 ymin,ymax (A): -3.616000 47.62100 zmin,zma (A): -24.43000 31.22800 x,y,z range (A): 39.99300 51.23700 55.65800 scale (grids/A): 0.6396205 object centre (A): 14.71950 22.00250 3.399000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.66448 92.88103 90.18027 assigned negative charge : -284.8263 centred at (gu) : 90.77226 93.00459 90.11570 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5518 nv = 96 ne = 84 npr = 40207 no. pairs analyzed = 40207 no. exposed pairs = 2461 no. arc points = 17428 no. surface atoms = 840 nbur = 1124 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 281 mr = 3085 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1807 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6536 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2582584E-10 1.0451825E-08 midg,1,midg; midg,igrid,midg 8.1099865E-09 -1.1315439E-08 1,midg,midg; igrid,midg,midg 1.1809502E-08 -5.1924429E-09 gauss-seidel spectral radius is 0.9872801 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 14:10:09 rms-change max change #iterations 0.1198783 20.07496 at 10iterations 1.1862739E-02 2.009605 at 20iterations 1.1625855E-03 0.1650124 at 30iterations 1.1474096E-04 1.7405510E-02 at 40iterations 1.1276820E-05 1.7318726E-03 at 50iterations finished qdiffx linear iterations at : 14:10:20 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 1.1276820E-05 1.7318726E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 14:10:22 4.059u 0.236s 0:17.12 25.0% 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 14:10:26 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918862 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): -5.277000 34.71600 ymin,ymax (A): -3.616000 47.62100 zmin,zma (A): -24.43000 31.22800 x,y,z range (A): 39.99300 51.23700 55.65800 scale (grids/A): 1.918862 object centre (A): 14.71950 22.00250 3.399000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.99361 98.64336 90.54076 assigned negative charge : -284.8263 centred at (gu) : 92.31702 99.01405 90.34710 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17428 grid for indexing accessible points = 1.400000 m= 21810 mr = 40734 m= 3376 mr = 16853 m= 181 mr = 2221 m= 0 mr = 69 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1035 time to turn everything in is 0.3200000 number of dielectric boundary points 24559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14415 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) : 0.6396205 object centre at (A) : 14.71950 22.00250 3.399000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6681609E-02 1.3733945E-02 midg,1,midg; midg,igrid,midg 2.9021019E-02 -8.7579014E-03 1,midg,midg; igrid,midg,midg 5.8122929E-03 -5.3831670E-03 gauss-seidel spectral radius is 0.9985747 estimated iterations to convergence 210 setup time was (sec) 0.5900000 now iterating at: 14:10:31 rms-change max change #iterations 3.610360 147.4607 at 10iterations 1.659446 68.01382 at 20iterations 0.7664422 27.61707 at 30iterations 0.3544803 13.09795 at 40iterations 0.1621479 5.641735 at 50iterations 7.4850917E-02 2.541348 at 60iterations 3.4368724E-02 1.213911 at 70iterations 1.5859842E-02 0.5699935 at 80iterations 7.2795330E-03 0.2639580 at 90iterations 3.3720797E-03 0.1148243 at 100iterations 1.5442361E-03 5.2737236E-02 at 110iterations 7.1369053E-04 2.4883032E-02 at 120iterations finished qdiffx linear iterations at : 14:10:58 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 7.1369053E-04 2.4883032E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 14:11:01 9.435u 0.313s 0:34.80 27.9% 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 14:11:03 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.878292 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): -5.277000 34.71600 ymin,ymax (A): -3.616000 47.62100 zmin,zma (A): -24.43000 31.22800 x,y,z range (A): 39.99300 51.23700 55.65800 scale (grids/A): 2.878292 object centre (A): 14.71950 22.00250 3.399000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.99035 102.9650 90.81100 assigned negative charge : -284.8263 centred at (gu) : 93.47562 103.5212 90.52072 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 136225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17428 grid for indexing accessible points = 1.400000 m= 70094 mr = 98454 m= 26398 mr = 58352 m= 6137 mr = 22131 m= 732 mr = 4774 m= 36 mr = 528 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 3806 time to turn everything in is 0.8400000 number of dielectric boundary points 55370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 14655 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) : 1.918862 object centre at (A) : 14.71950 22.00250 3.399000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.064868 3.4047019E-02 midg,1,midg; midg,igrid,midg 0.3099884 -0.1134385 1,midg,midg; igrid,midg,midg 2.9559106E-02 -3.0042171E-02 gauss-seidel spectral radius is 0.9992286 estimated iterations to convergence 284 setup time was (sec) 1.150000 now iterating at: 14:11:09 rms-change max change #iterations 8.438271 332.9781 at 10iterations 4.832122 128.4456 at 20iterations 2.745726 60.10807 at 30iterations 1.561615 31.50298 at 40iterations 0.8850787 16.92346 at 50iterations 0.5020879 10.88177 at 60iterations 0.2852904 5.909952 at 70iterations 0.1615438 3.138475 at 80iterations 9.1602974E-02 1.895175 at 90iterations 5.1818818E-02 1.026257 at 100iterations 2.9409202E-02 0.5950661 at 110iterations 1.6670857E-02 0.3584979 at 120iterations 9.4435979E-03 0.1940608 at 130iterations 5.3627705E-03 0.1054144 at 140iterations 3.0294403E-03 5.9525490E-02 at 150iterations 1.7218569E-03 3.7364960E-02 at 160iterations 9.7672024E-04 2.1029472E-02 at 170iterations 5.5222464E-04 1.1047363E-02 at 180iterations finished qdiffx linear iterations at : 14:11:50 total time elapsed so far: 14.50000 # loops : 180 mean,max change (kT/e) : 5.5222464E-04 1.1047363E-02 energy calculations done at 14.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.63000 DelPhi exited at 14:11:55 14.630u 0.340s 0:53.20 28.1% 0+0k 0+0io 0pf+0w