Sat Oct 8 17:07:13 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 17:07:13 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 = 3516 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5173817 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): -14.66900 44.43500 ymin,ymax (A): -39.35400 29.45400 zmin,zma (A): -16.62700 35.08300 x,y,z range (A): 59.10400 68.80800 51.71000 scale (grids/A): 0.5173817 object centre (A): 14.88300 -4.950000 9.228000 number of atom coordinates read : 3516 total number of charged atoms : 3370 net assigned charge : -3.999992 assigned positive charge : 528.5111 centred at (gu) : 90.62264 91.95785 90.51936 assigned negative charge : -532.5128 centred at (gu) : 90.63864 91.95361 90.47754 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5928 nv = 96 ne = 84 npr = 71724 no. pairs analyzed = 71724 no. exposed pairs = 4327 no. arc points = 29884 no. surface atoms = 1458 nbur = 2058 mkacc time = 0.2400000 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 = 1.680000 m= 213 mr = 3129 m= 0 mr = 5 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 3007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3029 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 8024 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6121447E-10 3.4754370E-11 midg,1,midg; midg,igrid,midg -5.3525875E-11 -1.0825740E-10 1,midg,midg; igrid,midg,midg -3.0869654E-11 -1.3826928E-10 gauss-seidel spectral radius is 0.9807987 estimated iterations to convergence 60 setup time was (sec) 0.8200000 now iterating at: 17:07:14 rms-change max change #iterations 5.9142854E-02 9.419802 at 10iterations 3.6050221E-03 0.7169828 at 20iterations 4.4680844E-04 7.6713562E-02 at 30iterations 1.1331072E-04 2.1372795E-02 at 40iterations 3.2472373E-05 6.1540604E-03 at 50iterations finished qdiffx linear iterations at : 17:07:18 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 3.2472373E-05 6.1540604E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.710000 DelPhi exited at 17:07:18 4.717u 0.433s 0:05.41 95.0% 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 Sat Oct 8 2011 at 17:07:18 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 = 3516 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.552145 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): -14.66900 44.43500 ymin,ymax (A): -39.35400 29.45400 zmin,zma (A): -16.62700 35.08300 x,y,z range (A): 59.10400 68.80800 51.71000 scale (grids/A): 1.552145 object centre (A): 14.88300 -4.950000 9.228000 number of atom coordinates read : 3516 total number of charged atoms : 3370 net assigned charge : -3.999992 assigned positive charge : 528.5111 centred at (gu) : 91.86649 95.87274 91.55699 assigned negative charge : -532.5128 centred at (gu) : 91.91556 95.86030 91.43188 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 67092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29884 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19881 mr = 46320 m= 1845 mr = 13543 m= 41 mr = 854 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 167 time to turn everything in is 0.7100000 number of dielectric boundary points 28142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 410 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 25460 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) : 0.5173817 object centre at (A) : 14.88300 -4.950000 9.228000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1938146E-03 2.2740699E-03 midg,1,midg; midg,igrid,midg 1.0159626E-02 2.0495907E-03 1,midg,midg; igrid,midg,midg -3.9399043E-03 -1.1602829E-02 gauss-seidel spectral radius is 0.9980283 estimated iterations to convergence 179 setup time was (sec) 1.040000 now iterating at: 17:07:20 rms-change max change #iterations 3.244170 159.9576 at 10iterations 1.302879 52.69554 at 20iterations 0.5232393 19.86051 at 30iterations 0.2113803 7.724070 at 40iterations 8.4847324E-02 3.054127 at 50iterations 3.4238555E-02 1.217059 at 60iterations 1.3841731E-02 0.5516196 at 70iterations 5.5921464E-03 0.2357330 at 80iterations 2.2734983E-03 8.8241577E-02 at 90iterations 9.3602372E-04 3.1482697E-02 at 100iterations 3.9996931E-04 1.4793396E-02 at 110iterations 1.8191892E-04 8.0890656E-03 at 120iterations finished qdiffx linear iterations at : 17:07:29 total time elapsed so far: 9.920000 # loops : 120 mean,max change (kT/e) : 1.8191892E-04 8.0890656E-03 energy calculations done at 9.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.13000 DelPhi exited at 17:07:29 10.139u 0.469s 0:10.93 96.8% 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 17:07:29 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 = 3516 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.328218 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): -14.66900 44.43500 ymin,ymax (A): -39.35400 29.45400 zmin,zma (A): -16.62700 35.08300 x,y,z range (A): 59.10400 68.80800 51.71000 scale (grids/A): 2.328218 object centre (A): 14.88300 -4.950000 9.228000 number of atom coordinates read : 3516 total number of charged atoms : 3370 net assigned charge : -3.999992 assigned positive charge : 528.5111 centred at (gu) : 92.79963 98.80907 92.33531 assigned negative charge : -532.5128 centred at (gu) : 92.87305 98.79040 92.14775 start vw surface at 0.1800000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 156214 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29884 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70782 mr = 113324 m= 18485 mr = 56129 m= 2602 mr = 13545 m= 159 mr = 1633 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 612 time to turn everything in is 2.000000 number of dielectric boundary points 63559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 26890 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) : 1.552145 object centre at (A) : 14.88300 -4.950000 9.228000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9596003E-02 4.1632969E-02 midg,1,midg; midg,igrid,midg 0.3408462 8.5768336E-03 1,midg,midg; igrid,midg,midg -5.3144477E-02 -0.1573896 gauss-seidel spectral radius is 0.9990948 estimated iterations to convergence 263 setup time was (sec) 2.360000 now iterating at: 17:07:32 rms-change max change #iterations 8.613453 254.9919 at 10iterations 4.738917 120.6014 at 20iterations 2.594887 58.64163 at 30iterations 1.418343 31.21222 at 40iterations 0.7727227 17.05800 at 50iterations 0.4205623 8.513020 at 60iterations 0.2283182 5.197968 at 70iterations 0.1239293 2.723543 at 80iterations 6.7218378E-02 1.525932 at 90iterations 3.6348864E-02 0.7917414 at 100iterations 1.9710142E-02 0.4965649 at 110iterations 1.0736920E-02 0.2187729 at 120iterations 5.8290558E-03 0.1260972 at 130iterations 3.1850673E-03 6.7489624E-02 at 140iterations 1.7432859E-03 3.5507202E-02 at 150iterations 9.6853822E-04 2.2441864E-02 at 160iterations 5.4895895E-04 1.3783216E-02 at 170iterations 3.2179328E-04 7.6942444E-03 at 180iterations finished qdiffx linear iterations at : 17:07:48 total time elapsed so far: 18.09000 # loops : 180 mean,max change (kT/e) : 3.2179328E-04 7.6942444E-03 energy calculations done at 18.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.32000 DelPhi exited at 17:07:48 18.321u 0.484s 0:19.09 98.4% 0+0k 0+0io 0pf+0w