Mon Oct 10 11:09:13 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 Mon Oct 10 2011 at 11:09:13 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7415431 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): -21.00800 24.21000 ymin,ymax (A): -8.080000 36.15200 zmin,zma (A): -3.643000 44.36500 x,y,z range (A): 45.21800 44.23199 48.00800 scale (grids/A): 0.7415431 object centre (A): 1.601000 14.03600 20.36100 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.07829 90.53930 90.21432 assigned negative charge : -323.3720 centred at (gu) : 89.11094 90.62057 90.40258 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7940 nv = 96 ne = 84 npr = 43739 no. pairs analyzed = 43739 no. exposed pairs = 2700 no. arc points = 19230 no. surface atoms = 908 nbur = 1209 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 529 mr = 4386 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.3100000 number of dielectric boundary points 3980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1582 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8462 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8782520E-08 -3.2915952E-07 midg,1,midg; midg,igrid,midg -2.5884145E-08 -2.2104179E-07 1,midg,midg; igrid,midg,midg -9.2702507E-08 -1.2517812E-07 gauss-seidel spectral radius is 0.9905241 estimated iterations to convergence 83 setup time was (sec) 0.5800000 now iterating at: 11:09:14 rms-change max change #iterations 0.2463081 43.63239 at 10iterations 3.3389837E-02 4.638630 at 20iterations 4.5096427E-03 0.6481152 at 30iterations 6.1016408E-04 7.5416565E-02 at 40iterations 8.2880404E-05 1.1054993E-02 at 50iterations finished qdiffx linear iterations at : 11:09:17 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 8.2880404E-05 1.1054993E-02 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 11:09:18 4.014u 0.270s 0:04.56 93.8% 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 Mon Oct 10 2011 at 11:09:18 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.224629 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): -21.00800 24.21000 ymin,ymax (A): -8.080000 36.15200 zmin,zma (A): -3.643000 44.36500 x,y,z range (A): 45.21800 44.23199 48.00800 scale (grids/A): 2.224629 object centre (A): 1.601000 14.03600 20.36100 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.23492 91.61801 90.64307 assigned negative charge : -323.3720 centred at (gu) : 87.33287 91.86163 91.20789 start vw surface at 0.1400000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 83891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19230 grid for indexing accessible points = 1.400000 m= 33715 mr = 57728 m= 7213 mr = 25702 m= 768 mr = 5027 m= 22 mr = 454 m= 0 mr = 8 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 4396 time to turn everything in is 0.7600000 number of dielectric boundary points 36690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 15756 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) : 0.7415431 object centre at (A) : 1.601000 14.03600 20.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7889175E-03 -0.1356069 midg,1,midg; midg,igrid,midg -2.5119327E-02 -3.4911647E-02 1,midg,midg; igrid,midg,midg 2.6888566E-03 -1.1041526E-02 gauss-seidel spectral radius is 0.9989313 estimated iterations to convergence 242 setup time was (sec) 1.050000 now iterating at: 11:09:19 rms-change max change #iterations 5.090275 226.5930 at 10iterations 2.585761 78.23231 at 20iterations 1.319062 37.22892 at 30iterations 0.6749030 21.38057 at 40iterations 0.3430654 9.632343 at 50iterations 0.1754804 4.724786 at 60iterations 8.9652836E-02 2.517651 at 70iterations 4.5603696E-02 1.366311 at 80iterations 2.3372917E-02 0.6562576 at 90iterations 1.1919750E-02 0.3665895 at 100iterations 6.0823131E-03 0.1776638 at 110iterations 3.0995233E-03 8.7318346E-02 at 120iterations finished qdiffx linear iterations at : 11:09:27 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 3.0995233E-03 8.7318346E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 11:09:28 9.596u 0.300s 0:10.15 97.4% 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 Mon Oct 10 2011 at 11:09:28 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.336944 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): -21.00800 24.21000 ymin,ymax (A): -8.080000 36.15200 zmin,zma (A): -3.643000 44.36500 x,y,z range (A): 45.21800 44.23199 48.00800 scale (grids/A): 3.336944 object centre (A): 1.601000 14.03600 20.36100 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 85.85245 92.42690 90.96462 assigned negative charge : -323.3720 centred at (gu) : 85.99936 92.79240 91.81174 start vw surface at 0.1500000 fill in re-entrant regions at 1.120000 boundary points on vw surface= 192929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19230 grid for indexing accessible points = 1.400000 m= 102989 mr = 138848 m= 44271 mr = 85279 m= 13891 mr = 37043 m= 3166 mr = 11068 m= 463 mr = 2458 m= 16 mr = 316 m= 0 mr = 4 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 14324 time to turn everything in is 2.500000 number of dielectric boundary points 82709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.650000 number of grid points assigned charge 15824 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) : 2.224629 object centre at (A) : 1.601000 14.03600 20.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5329400E-02 -1.275906 midg,1,midg; midg,igrid,midg -0.2306322 -0.1566893 1,midg,midg; igrid,midg,midg 7.3812746E-02 -0.1763611 gauss-seidel spectral radius is 0.9993194 estimated iterations to convergence 302 setup time was (sec) 2.830000 now iterating at: 11:09:31 rms-change max change #iterations 10.95456 311.0907 at 10iterations 6.424030 122.8308 at 20iterations 3.780935 63.25859 at 30iterations 2.214035 36.60486 at 40iterations 1.299376 21.03271 at 50iterations 0.7635099 12.89726 at 60iterations 0.4466929 7.394817 at 70iterations 0.2626885 4.436571 at 80iterations 0.1540121 2.556787 at 90iterations 9.0212688E-02 1.410433 at 100iterations 5.2979201E-02 0.8590670 at 110iterations 3.1100182E-02 0.5577393 at 120iterations 1.8230965E-02 0.3257408 at 130iterations 1.0717105E-02 0.1684981 at 140iterations 6.2866732E-03 9.6977711E-02 at 150iterations 3.6937459E-03 5.9557915E-02 at 160iterations 2.1629189E-03 3.7244797E-02 at 170iterations 1.2719339E-03 2.0723820E-02 at 180iterations finished qdiffx linear iterations at : 11:09:45 total time elapsed so far: 16.74000 # loops : 180 mean,max change (kT/e) : 1.2719339E-03 2.0723820E-02 energy calculations done at 16.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.92000 DelPhi exited at 11:09:45 16.917u 0.321s 0:17.51 98.4% 0+0k 0+0io 0pf+0w