Mon Oct 10 09:44:32 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 Mon Oct 10 2011 at 09:44:32 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: HIT 232 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5789654 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): -16.93800 36.11500 ymin,ymax (A): -64.34000 -4.700000 zmin,zma (A): -4.697000 56.79200 x,y,z range (A): 53.05300 59.64000 61.48900 scale (grids/A): 0.5789654 object centre (A): 9.588499 -34.52000 26.04750 number of atom coordinates read : 2925 total number of charged atoms : 2770 net assigned charge : 6.014020 assigned positive charge : 432.1857 centred at (gu) : 89.43370 89.26759 87.68510 assigned negative charge : -426.1722 centred at (gu) : 89.55109 89.22779 87.46700 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6546 nv = 96 ne = 84 npr = 56989 no. pairs analyzed = 56989 no. exposed pairs = 4469 no. arc points = 31810 no. surface atoms = 1479 nbur = 1446 mkacc time = 0.1300000 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= 328 mr = 2819 m= 4 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3127 ## 341 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8300 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5940923E-09 3.3081586E-09 midg,1,midg; midg,igrid,midg 6.5849159E-10 1.8346730E-09 1,midg,midg; igrid,midg,midg 4.2418740E-09 -8.9711399E-10 gauss-seidel spectral radius is 0.9846162 estimated iterations to convergence 66 setup time was (sec) 0.5900000 now iterating at: 09:44:32 rms-change max change #iterations 9.7550303E-02 14.62565 at 10iterations 7.5798198E-03 1.238037 at 20iterations 5.9294142E-04 0.1058197 at 30iterations 5.4621069E-05 8.0718994E-03 at 40iterations 7.4235691E-06 1.0604858E-03 at 50iterations finished qdiffx linear iterations at : 09:44:35 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 7.4235691E-06 1.0604858E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 09:44:36 3.590u 0.147s 0:04.34 85.9% 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 Mon Oct 10 2011 at 09:44:36 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: HIT 232 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.736896 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): -16.93800 36.11500 ymin,ymax (A): -64.34000 -4.700000 zmin,zma (A): -4.697000 56.79200 x,y,z range (A): 53.05300 59.64000 61.48900 scale (grids/A): 1.736896 object centre (A): 9.588499 -34.52000 26.04750 number of atom coordinates read : 2925 total number of charged atoms : 2770 net assigned charge : 6.014020 assigned positive charge : 432.1857 centred at (gu) : 88.30031 87.80236 83.05492 assigned negative charge : -426.1722 centred at (gu) : 88.65313 87.68279 82.40071 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31810 grid for indexing accessible points = 1.400000 m= 21779 mr = 42756 m= 2652 mr = 13533 m= 112 mr = 1080 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 37509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 21517 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) : 0.5789654 object centre at (A) : 9.588499 -34.52000 26.04750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5695734E-02 2.4331264E-02 midg,1,midg; midg,igrid,midg 2.2463374E-02 3.0845437E-02 1,midg,midg; igrid,midg,midg 1.4151948E-02 7.4072075E-03 gauss-seidel spectral radius is 0.9984168 estimated iterations to convergence 199 setup time was (sec) 0.8600000 now iterating at: 09:44:37 rms-change max change #iterations 3.746507 167.6323 at 10iterations 1.649488 59.04827 at 20iterations 0.7269466 27.36212 at 30iterations 0.3188056 11.66528 at 40iterations 0.1409604 4.831348 at 50iterations 6.2127516E-02 2.424263 at 60iterations 2.7303606E-02 0.9975395 at 70iterations 1.2023045E-02 0.3829260 at 80iterations 5.3155753E-03 0.1985741 at 90iterations 2.3507564E-03 8.0920100E-02 at 100iterations 1.0342012E-03 3.8335800E-02 at 110iterations 4.5820736E-04 1.5377998E-02 at 120iterations finished qdiffx linear iterations at : 09:44:44 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 4.5820736E-04 1.5377998E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 09:44:45 7.828u 0.245s 0:08.38 96.1% 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 Mon Oct 10 2011 at 09:44:45 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: HIT 232 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.605344 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): -16.93800 36.11500 ymin,ymax (A): -64.34000 -4.700000 zmin,zma (A): -4.697000 56.79200 x,y,z range (A): 53.05300 59.64000 61.48900 scale (grids/A): 2.605344 object centre (A): 9.588499 -34.52000 26.04750 number of atom coordinates read : 2925 total number of charged atoms : 2770 net assigned charge : 6.014020 assigned positive charge : 432.1857 centred at (gu) : 87.45024 86.70325 79.58215 assigned negative charge : -426.1722 centred at (gu) : 87.97946 86.52413 78.60094 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 162785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31810 grid for indexing accessible points = 1.400000 m= 72027 mr = 106113 m= 22771 mr = 53144 m= 4120 mr = 15808 m= 333 mr = 2355 m= 8 mr = 123 m= 0 mr = 2 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 84499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 22150 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) : 1.736896 object centre at (A) : 9.588499 -34.52000 26.04750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3838096 0.3299291 midg,1,midg; midg,igrid,midg 0.6013021 0.4416281 1,midg,midg; igrid,midg,midg 0.1431235 0.1244504 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 1.650000 now iterating at: 09:44:46 rms-change max change #iterations 9.574299 295.2345 at 10iterations 5.650257 159.0645 at 20iterations 3.289840 77.08031 at 30iterations 1.904782 51.13078 at 40iterations 1.096957 28.53958 at 50iterations 0.6290867 16.22986 at 60iterations 0.3605022 10.35893 at 70iterations 0.2060465 5.236412 at 80iterations 0.1176921 2.587181 at 90iterations 6.7043900E-02 1.437405 at 100iterations 3.8262494E-02 0.8144727 at 110iterations 2.1711079E-02 0.4803009 at 120iterations 1.2375365E-02 0.2785683 at 130iterations 7.0131659E-03 0.1449170 at 140iterations 3.9953976E-03 8.8325500E-02 at 150iterations 2.2663900E-03 4.8366547E-02 at 160iterations 1.2879362E-03 3.2038689E-02 at 170iterations 7.3154340E-04 1.4162064E-02 at 180iterations finished qdiffx linear iterations at : 09:44:57 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 7.3154340E-04 1.4162064E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 09:44:58 12.876u 0.223s 0:13.41 97.6% 0+0k 0+0io 0pf+0w