Sun Oct 9 18:23:00 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 18:23:00 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5293444 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): -8.168000 59.08500 ymin,ymax (A): -14.39300 34.10300 zmin,zma (A): 22.41700 70.43600 x,y,z range (A): 67.25301 48.49600 48.01900 scale (grids/A): 0.5293444 object centre (A): 25.45850 9.855000 46.42650 number of atom coordinates read : 2896 total number of charged atoms : 2748 net assigned charge : 6.906026 assigned positive charge : 441.1864 centred at (gu) : 89.62871 90.64733 88.74068 assigned negative charge : -434.2814 centred at (gu) : 89.65343 90.72588 88.65739 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5237 nv = 96 ne = 84 npr = 57157 no. pairs analyzed = 57157 no. exposed pairs = 3809 no. arc points = 26527 no. surface atoms = 1278 nbur = 1618 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 = 1.624000 m= 221 mr = 2589 m= 0 mr = 4 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2634 ## 347 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6889 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0577858E-11 3.6848247E-10 midg,1,midg; midg,igrid,midg 4.1623308E-10 -5.5654922E-11 1,midg,midg; igrid,midg,midg 3.3938735E-10 1.2862397E-10 gauss-seidel spectral radius is 0.9816056 estimated iterations to convergence 61 setup time was (sec) 0.5700000 now iterating at: 18:23:01 rms-change max change #iterations 6.1777432E-02 10.74681 at 10iterations 3.8330203E-03 0.5848217 at 20iterations 2.8551000E-04 6.1515808E-02 at 30iterations 3.2933622E-05 8.0890656E-03 at 40iterations 6.6280445E-06 1.3008118E-03 at 50iterations finished qdiffx linear iterations at : 18:23:03 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 6.6280445E-06 1.3008118E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 18:23:04 3.407u 0.151s 0:03.83 92.6% 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 18:23:04 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.588033 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): -8.168000 59.08500 ymin,ymax (A): -14.39300 34.10300 zmin,zma (A): 22.41700 70.43600 x,y,z range (A): 67.25301 48.49600 48.01900 scale (grids/A): 1.588033 object centre (A): 25.45850 9.855000 46.42650 number of atom coordinates read : 2896 total number of charged atoms : 2748 net assigned charge : 6.906026 assigned positive charge : 441.1864 centred at (gu) : 88.88538 91.94143 86.22121 assigned negative charge : -434.2814 centred at (gu) : 88.96013 92.17745 85.97175 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 58625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26527 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18183 mr = 39385 m= 1908 mr = 11892 m= 57 mr = 842 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 26652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 372 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 20879 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) : 0.5293444 object centre at (A) : 25.45850 9.855000 46.42650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4250879E-03 4.7583333E-03 midg,1,midg; midg,igrid,midg 5.4660682E-03 -4.6891407E-03 1,midg,midg; igrid,midg,midg 1.8419586E-02 3.2320109E-03 gauss-seidel spectral radius is 0.9980664 estimated iterations to convergence 181 setup time was (sec) 0.7600000 now iterating at: 18:23:05 rms-change max change #iterations 3.102334 175.1614 at 10iterations 1.263075 54.19434 at 20iterations 0.5106954 19.08637 at 30iterations 0.2074524 7.942006 at 40iterations 8.4493227E-02 3.621258 at 50iterations 3.4400448E-02 1.466553 at 60iterations 1.3966616E-02 0.5194473 at 70iterations 5.7047745E-03 0.2550297 at 80iterations 2.3367407E-03 9.1044426E-02 at 90iterations 9.5648947E-04 3.7889481E-02 at 100iterations 3.9944623E-04 1.5885353E-02 at 110iterations 1.7023395E-04 7.0343018E-03 at 120iterations finished qdiffx linear iterations at : 18:23:11 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 1.7023395E-04 7.0343018E-03 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 18:23:12 7.389u 0.162s 0:07.82 96.4% 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 18:23:12 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.382050 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): -8.168000 59.08500 ymin,ymax (A): -14.39300 34.10300 zmin,zma (A): 22.41700 70.43600 x,y,z range (A): 67.25301 48.49600 48.01900 scale (grids/A): 2.382050 object centre (A): 25.45850 9.855000 46.42650 number of atom coordinates read : 2896 total number of charged atoms : 2748 net assigned charge : 6.906026 assigned positive charge : 441.1864 centred at (gu) : 88.32771 92.91216 84.33147 assigned negative charge : -434.2814 centred at (gu) : 88.44012 93.26597 83.95761 start vw surface at 0.1700000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 136139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26527 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 62849 mr = 96596 m= 17840 mr = 48580 m= 2837 mr = 12834 m= 205 mr = 1699 m= 3 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 60089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 21960 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) : 1.588033 object centre at (A) : 25.45850 9.855000 46.42650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7143271E-02 6.2050223E-02 midg,1,midg; midg,igrid,midg 0.1047502 -0.1028271 1,midg,midg; igrid,midg,midg 0.8373114 5.1726408E-02 gauss-seidel spectral radius is 0.9990970 estimated iterations to convergence 263 setup time was (sec) 1.370000 now iterating at: 18:23:13 rms-change max change #iterations 8.258612 292.8321 at 10iterations 4.637455 124.2561 at 20iterations 2.574440 82.48347 at 30iterations 1.425240 37.35619 at 40iterations 0.7838791 21.00703 at 50iterations 0.4301305 9.883442 at 60iterations 0.2366269 5.614449 at 70iterations 0.1288529 3.080444 at 80iterations 7.0307478E-02 1.710929 at 90iterations 3.8424715E-02 0.8988403 at 100iterations 2.0976588E-02 0.4941940 at 110iterations 1.1426455E-02 0.2854919 at 120iterations 6.2188278E-03 0.1565380 at 130iterations 3.3973565E-03 7.5232387E-02 at 140iterations 1.8547025E-03 4.3304443E-02 at 150iterations 1.0213986E-03 2.2647858E-02 at 160iterations 5.7245669E-04 1.4907837E-02 at 170iterations 3.3459000E-04 8.5420609E-03 at 180iterations finished qdiffx linear iterations at : 18:23:23 total time elapsed so far: 11.40000 # loops : 180 mean,max change (kT/e) : 3.3459000E-04 8.5420609E-03 energy calculations done at 11.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.59000 DelPhi exited at 18:23:24 11.595u 0.178s 0:12.03 97.7% 0+0k 0+0io 0pf+0w