Tue Oct 11 06:22:47 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 Tue Oct 11 2011 at 06:22:47 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2052 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7194681 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): 3.368000 47.18200 ymin,ymax (A): 0.6660000 42.34400 zmin,zma (A): -2.570000 46.91100 x,y,z range (A): 43.81400 41.67800 49.48100 scale (grids/A): 0.7194681 object centre (A): 25.27500 21.50500 22.17050 number of atom coordinates read : 2052 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.86723 89.91496 90.32112 assigned negative charge : -304.4261 centred at (gu) : 90.05967 89.89800 90.34934 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7266 nv = 96 ne = 84 npr = 41194 no. pairs analyzed = 41194 no. exposed pairs = 2463 no. arc points = 16886 no. surface atoms = 840 nbur = 1212 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 480 mr = 4236 m= 8 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3447 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1569 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7938 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9546845E-08 6.3192992E-08 midg,1,midg; midg,igrid,midg 6.7766855E-08 8.6652186E-08 1,midg,midg; igrid,midg,midg 2.0113478E-07 -4.4554849E-08 gauss-seidel spectral radius is 0.9899245 estimated iterations to convergence 81 setup time was (sec) 0.3500000 now iterating at: 06:22:47 rms-change max change #iterations 0.2207707 28.88064 at 10iterations 2.8437685E-02 3.835793 at 20iterations 3.9619571E-03 0.4899607 at 30iterations 6.7753182E-04 8.9511871E-02 at 40iterations 1.6536754E-04 2.3330688E-02 at 50iterations finished qdiffx linear iterations at : 06:22:50 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.6536754E-04 2.3330688E-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) 3.320000 DelPhi exited at 06:22:51 3.326u 0.174s 0:04.47 78.0% 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 Tue Oct 11 2011 at 06:22:51 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2052 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.158404 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): 3.368000 47.18200 ymin,ymax (A): 0.6660000 42.34400 zmin,zma (A): -2.570000 46.91100 x,y,z range (A): 43.81400 41.67800 49.48100 scale (grids/A): 2.158404 object centre (A): 25.27500 21.50500 22.17050 number of atom coordinates read : 2052 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.60165 89.74468 90.96344 assigned negative charge : -304.4261 centred at (gu) : 90.17905 89.69408 91.04797 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16886 grid for indexing accessible points = 1.400000 m= 31143 mr = 55221 m= 6174 mr = 23819 m= 590 mr = 4105 m= 16 mr = 291 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15291 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) : 0.7194681 object centre at (A) : 25.27500 21.50500 22.17050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6945950E-02 6.7076690E-02 midg,1,midg; midg,igrid,midg 4.3250713E-03 2.6980409E-02 1,midg,midg; igrid,midg,midg 5.0845284E-02 7.5803748E-03 gauss-seidel spectral radius is 0.9988629 estimated iterations to convergence 235 setup time was (sec) 0.6100000 now iterating at: 06:22:52 rms-change max change #iterations 4.691866 200.2556 at 10iterations 2.338058 79.35961 at 20iterations 1.177039 36.40443 at 30iterations 0.5895090 17.68943 at 40iterations 0.2957799 9.453424 at 50iterations 0.1484884 4.330788 at 60iterations 7.4544981E-02 2.204559 at 70iterations 3.7301410E-02 1.157557 at 80iterations 1.8787067E-02 0.5921631 at 90iterations 9.5859664E-03 0.2907352 at 100iterations 4.9194130E-03 0.1597290 at 110iterations 2.5565182E-03 7.1714401E-02 at 120iterations finished qdiffx linear iterations at : 06:22:59 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.5565182E-03 7.1714401E-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) 7.760000 DelPhi exited at 06:23:00 7.758u 0.184s 0:08.42 94.1% 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 Tue Oct 11 2011 at 06:23:00 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2052 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.237606 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): 3.368000 47.18200 ymin,ymax (A): 0.6660000 42.34400 zmin,zma (A): -2.570000 46.91100 x,y,z range (A): 43.81400 41.67800 49.48100 scale (grids/A): 3.237606 object centre (A): 25.27500 21.50500 22.17050 number of atom coordinates read : 2052 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.40256 89.61698 91.44520 assigned negative charge : -304.4261 centred at (gu) : 90.26862 89.54126 91.57212 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 177914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16886 grid for indexing accessible points = 1.400000 m= 97050 mr = 132765 m= 39684 mr = 81144 m= 11690 mr = 32924 m= 2353 mr = 8983 m= 278 mr = 1665 m= 10 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 71315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 15384 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) : 2.158404 object centre at (A) : 25.27500 21.50500 22.17050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4663191 0.6163789 midg,1,midg; midg,igrid,midg -2.4198230E-02 0.2021285 1,midg,midg; igrid,midg,midg 0.3504158 0.1694406 gauss-seidel spectral radius is 0.9992997 estimated iterations to convergence 298 setup time was (sec) 1.400000 now iterating at: 06:23:02 rms-change max change #iterations 10.33893 401.5996 at 10iterations 6.140767 131.9354 at 20iterations 3.634953 89.28197 at 30iterations 2.144943 43.55580 at 40iterations 1.265183 24.65808 at 50iterations 0.7459120 15.25758 at 60iterations 0.4392439 7.785378 at 70iterations 0.2582388 4.341843 at 80iterations 0.1515740 2.723869 at 90iterations 8.9434087E-02 1.607427 at 100iterations 5.2811518E-02 0.9724979 at 110iterations 3.1415384E-02 0.6475983 at 120iterations 1.8922141E-02 0.3266411 at 130iterations 1.1683325E-02 0.2277527 at 140iterations 7.4897041E-03 0.1364918 at 150iterations 5.0429539E-03 9.3719482E-02 at 160iterations 3.6034689E-03 6.8031311E-02 at 170iterations 2.7169962E-03 5.2757263E-02 at 180iterations finished qdiffx linear iterations at : 06:23:13 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 2.7169962E-03 5.2757263E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 06:23:13 12.718u 0.228s 0:13.35 96.8% 0+0k 0+0io 0pf+0w