Sat Oct 8 19:44:44 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 8 2011 at 19:44:44 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 = 2588 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6170592 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): -10.49500 38.81900 ymin,ymax (A): -22.05900 26.86100 zmin,zma (A): -12.53200 45.16100 x,y,z range (A): 49.31400 48.92000 57.69300 scale (grids/A): 0.6170592 object centre (A): 14.16200 2.401000 16.31450 number of atom coordinates read : 2588 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 88.45551 88.60635 89.61208 assigned negative charge : -386.5045 centred at (gu) : 88.34986 88.68457 89.49971 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6397 nv = 96 ne = 84 npr = 54210 no. pairs analyzed = 54210 no. exposed pairs = 3004 no. arc points = 21604 no. surface atoms = 1008 nbur = 1580 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 3566 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.3100000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2165 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7994 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6427631E-09 8.5753564E-09 midg,1,midg; midg,igrid,midg 9.9989652E-09 -1.5300452E-09 1,midg,midg; igrid,midg,midg -5.5055143E-09 6.3714287E-09 gauss-seidel spectral radius is 0.9863952 estimated iterations to convergence 70 setup time was (sec) 0.5700000 now iterating at: 19:44:45 rms-change max change #iterations 0.1228906 19.75386 at 10iterations 1.1417388E-02 1.753250 at 20iterations 1.0384191E-03 0.1498432 at 30iterations 9.3009781E-05 1.3492584E-02 at 40iterations 8.5047259E-06 1.1758804E-03 at 50iterations finished qdiffx linear iterations at : 19:44:49 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 8.5047259E-06 1.1758804E-03 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 19:44:49 4.686u 0.379s 0:05.32 94.9% 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 Sat Oct 8 2011 at 19:44:49 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 = 2588 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.851178 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): -10.49500 38.81900 ymin,ymax (A): -22.05900 26.86100 zmin,zma (A): -12.53200 45.16100 x,y,z range (A): 49.31400 48.92000 57.69300 scale (grids/A): 1.851178 object centre (A): 14.16200 2.401000 16.31450 number of atom coordinates read : 2588 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 85.36605 85.81856 88.83564 assigned negative charge : -386.5045 centred at (gu) : 85.04947 86.05352 88.49890 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21604 grid for indexing accessible points = 1.400000 m= 23689 mr = 48387 m= 3214 mr = 17390 m= 147 mr = 1895 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 4589 time to turn everything in is 0.5800000 number of dielectric boundary points 28884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19224 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) : 0.6170592 object centre at (A) : 14.16200 2.401000 16.31450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0155771E-02 2.3170145E-02 midg,1,midg; midg,igrid,midg 1.9506343E-02 5.6433775E-03 1,midg,midg; igrid,midg,midg -4.8606233E-03 3.1346854E-02 gauss-seidel spectral radius is 0.9985511 estimated iterations to convergence 208 setup time was (sec) 0.9000000 now iterating at: 19:44:50 rms-change max change #iterations 3.971434 159.6960 at 10iterations 1.815757 66.51172 at 20iterations 0.8297853 29.25559 at 30iterations 0.3791620 12.20030 at 40iterations 0.1745866 5.860863 at 50iterations 7.9856478E-02 2.864421 at 60iterations 3.6527500E-02 1.302605 at 70iterations 1.6639575E-02 0.5615273 at 80iterations 7.6377583E-03 0.2704344 at 90iterations 3.5075604E-03 0.1338882 at 100iterations 1.6028595E-03 5.0497055E-02 at 110iterations 7.3399302E-04 2.3782730E-02 at 120iterations finished qdiffx linear iterations at : 19:45:00 total time elapsed so far: 10.54000 # loops : 120 mean,max change (kT/e) : 7.3399302E-04 2.3782730E-02 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 19:45:01 10.713u 0.416s 0:11.39 97.6% 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 Sat Oct 8 2011 at 19:45:01 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 = 2588 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.776767 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): -10.49500 38.81900 ymin,ymax (A): -22.05900 26.86100 zmin,zma (A): -12.53200 45.16100 x,y,z range (A): 49.31400 48.92000 57.69300 scale (grids/A): 2.776767 object centre (A): 14.16200 2.401000 16.31450 number of atom coordinates read : 2588 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 83.04899 83.72759 88.25351 assigned negative charge : -386.5045 centred at (gu) : 82.57418 84.08030 87.74837 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 161113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21604 grid for indexing accessible points = 1.400000 m= 78537 mr = 117179 m= 25825 mr = 64397 m= 5498 mr = 20581 m= 653 mr = 4049 m= 29 mr = 424 m= 0 mr = 8 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 15942 time to turn everything in is 1.430000 number of dielectric boundary points 65017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 19621 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) : 1.851178 object centre at (A) : 14.16200 2.401000 16.31450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1507879 0.2708065 midg,1,midg; midg,igrid,midg 0.2302509 0.1384023 1,midg,midg; igrid,midg,midg -2.1785658E-02 0.3944243 gauss-seidel spectral radius is 0.9992289 estimated iterations to convergence 284 setup time was (sec) 1.760000 now iterating at: 19:45:03 rms-change max change #iterations 9.368995 345.5941 at 10iterations 5.372440 190.0057 at 20iterations 3.064286 74.52580 at 30iterations 1.745579 44.40060 at 40iterations 0.9929429 20.71648 at 50iterations 0.5652823 11.95410 at 60iterations 0.3216824 6.237997 at 70iterations 0.1826071 4.215719 at 80iterations 0.1034723 1.961951 at 90iterations 5.8797318E-02 1.153313 at 100iterations 3.3418141E-02 0.6453958 at 110iterations 1.8940600E-02 0.3855686 at 120iterations 1.0735291E-02 0.2285004 at 130iterations 6.0874592E-03 0.1055603 at 140iterations 3.4591332E-03 6.7760468E-02 at 150iterations 1.9650895E-03 3.9390564E-02 at 160iterations 1.1136716E-03 2.0263672E-02 at 170iterations 6.3157448E-04 1.3210297E-02 at 180iterations finished qdiffx linear iterations at : 19:45:19 total time elapsed so far: 17.94000 # loops : 180 mean,max change (kT/e) : 6.3157448E-04 1.3210297E-02 energy calculations done at 17.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.12000 DelPhi exited at 19:45:19 18.124u 0.457s 0:18.85 98.5% 0+0k 0+0io 0pf+0w