Tue Oct 11 08:34:24 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 Tue Oct 11 2011 at 08:34:24 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 = 2057 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: 0.7446453 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): -4.238000 43.57000 ymin,ymax (A): -21.90800 25.51600 zmin,zma (A): 6.070000 48.38900 x,y,z range (A): 47.80800 47.42400 42.31900 scale (grids/A): 0.7446453 object centre (A): 19.66600 1.803999 27.22950 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.98248 88.94604 90.03032 assigned negative charge : -304.2972 centred at (gu) : 90.85860 89.05831 89.98683 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7783 nv = 96 ne = 84 npr = 41751 no. pairs analyzed = 41751 no. exposed pairs = 2415 no. arc points = 16961 no. surface atoms = 822 nbur = 1235 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 541 mr = 4554 m= 6 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1456 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 8253 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6357816E-08 1.9010746E-07 midg,1,midg; midg,igrid,midg 3.1721524E-07 2.0229376E-08 1,midg,midg; igrid,midg,midg 9.9565387E-09 3.2754409E-07 gauss-seidel spectral radius is 0.9905879 estimated iterations to convergence 84 setup time was (sec) 0.5200000 now iterating at: 08:34:25 rms-change max change #iterations 0.2493582 35.95264 at 10iterations 3.3624031E-02 3.991736 at 20iterations 4.7772252E-03 0.5793104 at 30iterations 7.3119841E-04 0.1069565 at 40iterations 1.4403896E-04 1.8733978E-02 at 50iterations finished qdiffx linear iterations at : 08:34:29 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 1.4403896E-04 1.8733978E-02 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 08:34:29 4.564u 0.359s 0:05.42 90.5% 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 08:34:29 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 = 2057 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: 2.233936 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): -4.238000 43.57000 ymin,ymax (A): -21.90800 25.51600 zmin,zma (A): 6.070000 48.38900 x,y,z range (A): 47.80800 47.42400 42.31900 scale (grids/A): 2.233936 object centre (A): 19.66600 1.803999 27.22950 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 92.94746 86.83825 90.09105 assigned negative charge : -304.2972 centred at (gu) : 92.57594 87.17508 89.96063 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16961 grid for indexing accessible points = 1.400000 m= 34399 mr = 58866 m= 7331 mr = 26556 m= 806 mr = 5022 m= 25 mr = 412 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 33726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15335 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) : 0.7446453 object centre at (A) : 19.66600 1.803999 27.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3034015E-02 2.9132800E-02 midg,1,midg; midg,igrid,midg 4.6836637E-02 -4.6953235E-02 1,midg,midg; igrid,midg,midg 6.4297460E-02 0.1313647 gauss-seidel spectral radius is 0.9989248 estimated iterations to convergence 241 setup time was (sec) 1.070000 now iterating at: 08:34:31 rms-change max change #iterations 5.008126 212.2582 at 10iterations 2.547724 86.96164 at 20iterations 1.304419 41.49654 at 30iterations 0.6656066 18.80525 at 40iterations 0.3403062 10.27872 at 50iterations 0.1736660 4.980644 at 60iterations 8.8641264E-02 2.450698 at 70iterations 4.5350228E-02 1.316149 at 80iterations 2.3255501E-02 0.6821346 at 90iterations 1.1948694E-02 0.3255463 at 100iterations 6.1343908E-03 0.1821167 at 110iterations 3.1675738E-03 9.1811180E-02 at 120iterations finished qdiffx linear iterations at : 08:34:42 total time elapsed so far: 12.37000 # loops : 120 mean,max change (kT/e) : 3.1675738E-03 9.1811180E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 08:34:43 12.545u 0.435s 0:13.29 97.5% 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 08:34:43 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 = 2057 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: 3.350904 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): -4.238000 43.57000 ymin,ymax (A): -21.90800 25.51600 zmin,zma (A): 6.070000 48.38900 x,y,z range (A): 47.80800 47.42400 42.31900 scale (grids/A): 3.350904 object centre (A): 19.66600 1.803999 27.22950 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 94.42111 85.25738 90.13658 assigned negative charge : -304.2972 centred at (gu) : 93.86396 85.76266 89.94108 start vw surface at 0.1100000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 188829 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16961 grid for indexing accessible points = 1.400000 m= 105339 mr = 141164 m= 45124 mr = 88610 m= 14084 mr = 37670 m= 3174 mr = 10921 m= 488 mr = 2325 m= 23 mr = 332 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.160000 number of dielectric boundary points 76034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 15432 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) : 2.233936 object centre at (A) : 19.66600 1.803999 27.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2205021 0.1295469 midg,1,midg; midg,igrid,midg 0.3846265 -0.5964037 1,midg,midg; igrid,midg,midg 0.5841988 1.056180 gauss-seidel spectral radius is 0.9993203 estimated iterations to convergence 303 setup time was (sec) 2.510000 now iterating at: 08:34:46 rms-change max change #iterations 10.89156 354.8555 at 10iterations 6.515701 133.3847 at 20iterations 3.885879 73.16174 at 30iterations 2.315250 48.30013 at 40iterations 1.374665 25.58695 at 50iterations 0.8148381 13.55239 at 60iterations 0.4831006 8.660299 at 70iterations 0.2857051 4.632362 at 80iterations 0.1691912 2.721227 at 90iterations 9.9905722E-02 1.598280 at 100iterations 5.9222177E-02 0.9988947 at 110iterations 3.5129834E-02 0.5487671 at 120iterations 2.0942368E-02 0.3473625 at 130iterations 1.2556141E-02 0.2042866 at 140iterations 7.6681552E-03 0.1384506 at 150iterations 4.7954721E-03 9.1117859E-02 at 160iterations 3.1144342E-03 5.4805756E-02 at 170iterations 2.1422461E-03 3.9695740E-02 at 180iterations finished qdiffx linear iterations at : 08:35:03 total time elapsed so far: 19.84000 # loops : 180 mean,max change (kT/e) : 2.1422461E-03 3.9695740E-02 energy calculations done at 19.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.01000 DelPhi exited at 08:35:04 20.011u 0.456s 0:20.89 97.9% 0+0k 0+0io 0pf+0w