Mon Oct 10 14:11:27 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 14:11:27 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 = 2039 !!! WARNING: ASP 175 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: 0.6706225 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): 7.138000 60.22300 ymin,ymax (A): 2.388000 50.05400 zmin,zma (A): 12.49000 55.81800 x,y,z range (A): 53.08500 47.66600 43.32800 scale (grids/A): 0.6706225 object centre (A): 33.68050 26.22100 34.15400 number of atom coordinates read : 2039 total number of charged atoms : 1904 net assigned charge : 3.728004 assigned positive charge : 303.6307 centred at (gu) : 87.61086 89.33583 89.81919 assigned negative charge : -299.9029 centred at (gu) : 87.75048 89.35875 89.87783 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6167 nv = 96 ne = 84 npr = 41437 no. pairs analyzed = 41437 no. exposed pairs = 2524 no. arc points = 17787 no. surface atoms = 854 nbur = 1185 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 373 mr = 3388 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1648 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7086 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4172142E-08 2.1717678E-11 midg,1,midg; midg,igrid,midg 1.8586308E-08 6.3147789E-09 1,midg,midg; igrid,midg,midg 6.4298398E-08 -9.8174837E-09 gauss-seidel spectral radius is 0.9884216 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 14:11:27 rms-change max change #iterations 0.1503983 21.64260 at 10iterations 1.6748404E-02 2.668045 at 20iterations 1.8252988E-03 0.2886536 at 30iterations 2.1614322E-04 3.1686783E-02 at 40iterations 3.2803560E-05 5.6457520E-03 at 50iterations finished qdiffx linear iterations at : 14:11:31 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 3.2803560E-05 5.6457520E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 14:11:31 4.120u 0.230s 0:04.77 91.1% 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 Mon Oct 10 2011 at 14:11:32 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 = 2039 !!! WARNING: ASP 175 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.011868 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): 7.138000 60.22300 ymin,ymax (A): 2.388000 50.05400 zmin,zma (A): 12.49000 55.81800 x,y,z range (A): 53.08500 47.66600 43.32800 scale (grids/A): 2.011868 object centre (A): 33.68050 26.22100 34.15400 number of atom coordinates read : 2039 total number of charged atoms : 1904 net assigned charge : 3.728004 assigned positive charge : 303.6307 centred at (gu) : 82.83229 88.00722 89.45758 assigned negative charge : -299.9029 centred at (gu) : 83.25124 88.07623 89.63332 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17787 grid for indexing accessible points = 1.400000 m= 24145 mr = 45681 m= 4247 mr = 17670 m= 341 mr = 2718 m= 7 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 28635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15041 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) : 0.6706225 object centre at (A) : 33.68050 26.22100 34.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7561549E-02 3.8123333E-03 midg,1,midg; midg,igrid,midg 3.4252740E-02 1.2199691E-02 1,midg,midg; igrid,midg,midg -2.9493518E-02 -4.7087688E-02 gauss-seidel spectral radius is 0.9987112 estimated iterations to convergence 221 setup time was (sec) 0.8400000 now iterating at: 14:11:33 rms-change max change #iterations 4.099480 215.6640 at 10iterations 1.957977 69.25507 at 20iterations 0.9314145 32.02951 at 30iterations 0.4482406 15.58566 at 40iterations 0.2147565 6.811467 at 50iterations 0.1028592 3.414375 at 60iterations 4.9190551E-02 1.566614 at 70iterations 2.3442524E-02 0.7846756 at 80iterations 1.1224926E-02 0.3666210 at 90iterations 5.4000551E-03 0.1785440 at 100iterations 2.5809873E-03 8.5435867E-02 at 110iterations 1.2341770E-03 4.1030884E-02 at 120iterations finished qdiffx linear iterations at : 14:11:41 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 1.2341770E-03 4.1030884E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.490000 DelPhi exited at 14:11:42 9.494u 0.238s 0:10.44 93.1% 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 Mon Oct 10 2011 at 14:11:42 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 = 2039 !!! WARNING: ASP 175 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.017802 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): 7.138000 60.22300 ymin,ymax (A): 2.388000 50.05400 zmin,zma (A): 12.49000 55.81800 x,y,z range (A): 53.08500 47.66600 43.32800 scale (grids/A): 3.017802 object centre (A): 33.68050 26.22100 34.15400 number of atom coordinates read : 2039 total number of charged atoms : 1904 net assigned charge : 3.728004 assigned positive charge : 303.6307 centred at (gu) : 79.24847 87.01086 89.18629 assigned negative charge : -299.9029 centred at (gu) : 79.87691 87.11424 89.45005 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 153107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17787 grid for indexing accessible points = 1.400000 m= 76984 mr = 110963 m= 28938 mr = 62799 m= 7928 mr = 23218 m= 1357 mr = 5883 m= 83 mr = 913 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 64595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 15232 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) : 2.011868 object centre at (A) : 33.68050 26.22100 34.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2832159 2.2288008E-02 midg,1,midg; midg,igrid,midg 0.2475927 1.6880346E-02 1,midg,midg; igrid,midg,midg -0.4946074 -0.5924600 gauss-seidel spectral radius is 0.9992691 estimated iterations to convergence 292 setup time was (sec) 1.650000 now iterating at: 14:11:44 rms-change max change #iterations 9.493063 369.8104 at 10iterations 5.575787 128.6205 at 20iterations 3.255968 74.14638 at 30iterations 1.899192 46.33901 at 40iterations 1.103798 23.74260 at 50iterations 0.6431553 13.30643 at 60iterations 0.3726325 7.855511 at 70iterations 0.2154879 4.355886 at 80iterations 0.1248980 2.357660 at 90iterations 7.2143480E-02 1.383236 at 100iterations 4.1882928E-02 0.7902069 at 110iterations 2.4060065E-02 0.4748573 at 120iterations 1.3935243E-02 0.2851334 at 130iterations 8.0371695E-03 0.1612368 at 140iterations 4.6507907E-03 8.7434769E-02 at 150iterations 2.6859909E-03 4.7271729E-02 at 160iterations 1.5554130E-03 3.1112194E-02 at 170iterations 8.9982036E-04 1.8501282E-02 at 180iterations finished qdiffx linear iterations at : 14:11:58 total time elapsed so far: 14.96000 # loops : 180 mean,max change (kT/e) : 8.9982036E-04 1.8501282E-02 energy calculations done at 14.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.15000 DelPhi exited at 14:11:58 15.147u 0.268s 0:15.78 97.5% 0+0k 0+0io 0pf+0w