Sun Oct 9 18:13:46 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 18:13:46 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 !!! WARNING: GLM 72 has a net charge of -0.0940 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: 0.5575306 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): -8.106999 55.74600 ymin,ymax (A): -14.41600 34.11600 zmin,zma (A): 22.50700 70.51300 x,y,z range (A): 63.85300 48.53200 48.00600 scale (grids/A): 0.5575306 object centre (A): 23.81950 9.850000 46.51000 number of atom coordinates read : 2896 total number of charged atoms : 2748 net assigned charge : 5.906021 assigned positive charge : 439.9944 centred at (gu) : 90.24798 90.68611 88.60936 assigned negative charge : -434.0893 centred at (gu) : 90.30362 90.77431 88.53345 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5950 nv = 96 ne = 84 npr = 57168 no. pairs analyzed = 57168 no. exposed pairs = 3801 no. arc points = 26478 no. surface atoms = 1281 nbur = 1615 mkacc time = 0.1400000 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 = 1.540000 m= 287 mr = 3042 m= 2 mr = 12 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 0.3200000 number of dielectric boundary points 3185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2661 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7638 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4654320E-10 9.5615138E-10 midg,1,midg; midg,igrid,midg 1.2320006E-09 -3.4784065E-10 1,midg,midg; igrid,midg,midg 1.0719773E-09 3.9390748E-11 gauss-seidel spectral radius is 0.9834018 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 18:13:47 rms-change max change #iterations 7.7948347E-02 15.08736 at 10iterations 5.6275157E-03 0.9644165 at 20iterations 5.5603194E-04 8.4579468E-02 at 30iterations 1.5740391E-04 2.1842957E-02 at 40iterations 7.5756150E-05 1.1097670E-02 at 50iterations finished qdiffx linear iterations at : 18:13:50 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 7.5756150E-05 1.1097670E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 18:13:50 3.406u 0.149s 0:03.83 92.4% 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 18:13:50 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 !!! WARNING: GLM 72 has a net charge of -0.0940 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: 1.672592 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): -8.106999 55.74600 ymin,ymax (A): -14.41600 34.11600 zmin,zma (A): 22.50700 70.51300 x,y,z range (A): 63.85300 48.53200 48.00600 scale (grids/A): 1.672592 object centre (A): 23.81950 9.850000 46.51000 number of atom coordinates read : 2896 total number of charged atoms : 2748 net assigned charge : 5.906021 assigned positive charge : 439.9944 centred at (gu) : 90.74301 92.05757 85.82718 assigned negative charge : -434.0893 centred at (gu) : 90.91065 92.32272 85.60008 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 65712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26478 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21706 mr = 44520 m= 2607 mr = 14710 m= 116 mr = 1301 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 29599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 21180 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) : 0.5575306 object centre at (A) : 23.81950 9.850000 46.51000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6886426E-03 6.5174615E-03 midg,1,midg; midg,igrid,midg 9.5389448E-03 -8.0826981E-03 1,midg,midg; igrid,midg,midg 2.2976168E-02 -5.5402191E-03 gauss-seidel spectral radius is 0.9982646 estimated iterations to convergence 191 setup time was (sec) 0.7900000 now iterating at: 18:13:51 rms-change max change #iterations 3.501560 165.5173 at 10iterations 1.482342 55.96980 at 20iterations 0.6322248 22.38834 at 30iterations 0.2690724 9.329943 at 40iterations 0.1148578 4.119987 at 50iterations 4.9250897E-02 1.825592 at 60iterations 2.0969797E-02 0.7770004 at 70iterations 8.9593213E-03 0.3172150 at 80iterations 3.8574671E-03 0.1466475 at 90iterations 1.6799670E-03 6.3310623E-02 at 100iterations 7.6510548E-04 2.6894093E-02 at 110iterations 3.8705135E-04 1.3956785E-02 at 120iterations finished qdiffx linear iterations at : 18:13:58 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 3.8705135E-04 1.3956785E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 18:13:58 7.581u 0.177s 0:08.02 96.6% 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 18:13:58 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 !!! WARNING: GLM 72 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.508888 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): -8.106999 55.74600 ymin,ymax (A): -14.41600 34.11600 zmin,zma (A): 22.50700 70.51300 x,y,z range (A): 63.85300 48.53200 48.00600 scale (grids/A): 2.508888 object centre (A): 23.81950 9.850000 46.51000 number of atom coordinates read : 2896 total number of charged atoms : 2748 net assigned charge : 5.906021 assigned positive charge : 439.9944 centred at (gu) : 91.11442 93.08606 83.74065 assigned negative charge : -434.0893 centred at (gu) : 91.36575 93.48402 83.39998 start vw surface at 0.1900000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 152328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26478 grid for indexing accessible points = 1.400000 m= 73259 mr = 109058 m= 22699 mr = 57341 m= 4225 mr = 16873 m= 363 mr = 2684 m= 3 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 66743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 21975 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) : 1.672592 object centre at (A) : 23.81950 9.850000 46.51000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1533576E-02 7.5125426E-02 midg,1,midg; midg,igrid,midg 0.1527894 -0.1573850 1,midg,midg; igrid,midg,midg 0.8935568 -6.4522915E-02 gauss-seidel spectral radius is 0.9991621 estimated iterations to convergence 273 setup time was (sec) 1.540000 now iterating at: 18:14:00 rms-change max change #iterations 9.006009 324.6766 at 10iterations 5.151795 135.0294 at 20iterations 2.933114 72.59141 at 30iterations 1.652526 38.15774 at 40iterations 0.9312794 24.77183 at 50iterations 0.5216821 12.05639 at 60iterations 0.2926389 7.056362 at 70iterations 0.1638509 4.900758 at 80iterations 9.1516405E-02 2.121717 at 90iterations 5.0991844E-02 1.077714 at 100iterations 2.8475367E-02 0.7066669 at 110iterations 1.5864367E-02 0.3661747 at 120iterations 8.8481642E-03 0.1989574 at 130iterations 4.9325181E-03 0.1197205 at 140iterations 2.7488752E-03 5.7741165E-02 at 150iterations 1.5345142E-03 3.8150787E-02 at 160iterations 8.6093199E-04 1.8804073E-02 at 170iterations 4.8589244E-04 9.4118118E-03 at 180iterations finished qdiffx linear iterations at : 18:14:10 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 4.8589244E-04 9.4118118E-03 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 18:14:11 11.908u 0.197s 0:12.37 97.7% 0+0k 0+0io 0pf+0w