Wed Dec 28 11:01:04 PST 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 Wed Dec 28 2011 at 11:01:04 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 0.5538959 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): -35.33400 10.64400 ymin,ymax (A): 0.5890001 42.77500 zmin,zma (A): -4.056000 60.21600 x,y,z range (A): 45.97800 42.18600 64.27200 scale (grids/A): 0.5538959 object centre (A): -12.34500 21.68200 28.08000 number of atom coordinates read : 1970 total number of charged atoms : 1836 net assigned charge : 3.362005 assigned positive charge : 290.4260 centred at (gu) : 90.17226 89.53577 89.99997 assigned negative charge : -287.0643 centred at (gu) : 90.07892 89.69695 89.99991 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4081 nv = 96 ne = 84 npr = 39277 no. pairs analyzed = 39277 no. exposed pairs = 2622 no. arc points = 18196 no. surface atoms = 903 nbur = 1067 mkacc time = 6.0000002E-02 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 = 1.568000 m= 159 mr = 2090 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1915 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5167 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7916805E-10 2.7985816E-10 midg,1,midg; midg,igrid,midg 1.3319426E-09 -5.9224842E-10 1,midg,midg; igrid,midg,midg -2.5191693E-10 8.4495455E-10 gauss-seidel spectral radius is 0.9831130 estimated iterations to convergence 63 setup time was (sec) 0.3600000 now iterating at: 11:01:04 rms-change max change #iterations 6.0233176E-02 14.62785 at 10iterations 4.1299779E-03 0.9333992 at 20iterations 2.8333656E-04 5.5610657E-02 at 30iterations 1.9560868E-05 4.0259361E-03 at 40iterations 1.3504495E-06 2.7275085E-04 at 50iterations finished qdiffx linear iterations at : 11:01:08 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 1.3504495E-06 2.7275085E-04 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 11:01:08 3.931u 0.185s 0:04.77 86.1% 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 Wed Dec 28 2011 at 11:01:08 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 1.661688 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): -35.33400 10.64400 ymin,ymax (A): 0.5890001 42.77500 zmin,zma (A): -4.056000 60.21600 x,y,z range (A): 45.97800 42.18600 64.27200 scale (grids/A): 1.661688 object centre (A): -12.34500 21.68200 28.08000 number of atom coordinates read : 1970 total number of charged atoms : 1836 net assigned charge : 3.362005 assigned positive charge : 290.4260 centred at (gu) : 90.51644 88.60722 90.00000 assigned negative charge : -287.0643 centred at (gu) : 90.23684 89.09115 89.99990 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 43762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18196 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15335 mr = 28917 m= 1818 mr = 11167 m= 67 mr = 1072 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 19809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14120 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) : 0.5538959 object centre at (A) : -12.34500 21.68200 28.08000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7121863E-02 1.7260026E-02 midg,1,midg; midg,igrid,midg 4.1175485E-03 -5.1698759E-03 1,midg,midg; igrid,midg,midg -1.0895929E-03 2.2434391E-04 gauss-seidel spectral radius is 0.9981316 estimated iterations to convergence 184 setup time was (sec) 0.5800000 now iterating at: 11:01:09 rms-change max change #iterations 2.673582 153.3891 at 10iterations 1.094817 49.56386 at 20iterations 0.4496558 19.22954 at 30iterations 0.1855798 7.519136 at 40iterations 7.6044664E-02 3.109688 at 50iterations 3.1332254E-02 1.399704 at 60iterations 1.2873227E-02 0.5103676 at 70iterations 5.2936976E-03 0.2209630 at 80iterations 2.1850655E-03 8.5163116E-02 at 90iterations 8.9691393E-04 3.6398888E-02 at 100iterations 3.6886474E-04 1.6326904E-02 at 110iterations 1.5201616E-04 6.6890717E-03 at 120iterations finished qdiffx linear iterations at : 11:01:19 total time elapsed so far: 10.19000 # loops : 120 mean,max change (kT/e) : 1.5201616E-04 6.6890717E-03 energy calculations done at 10.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.33000 DelPhi exited at 11:01:20 10.330u 0.331s 0:11.84 90.0% 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 Wed Dec 28 2011 at 11:01:20 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 2.492532 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): -35.33400 10.64400 ymin,ymax (A): 0.5890001 42.77500 zmin,zma (A): -4.056000 60.21600 x,y,z range (A): 45.97800 42.18600 64.27200 scale (grids/A): 2.492532 object centre (A): -12.34500 21.68200 28.08000 number of atom coordinates read : 1970 total number of charged atoms : 1836 net assigned charge : 3.362005 assigned positive charge : 290.4260 centred at (gu) : 90.77473 87.91081 89.99997 assigned negative charge : -287.0643 centred at (gu) : 90.35537 88.63687 89.99993 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 101166 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18196 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 50478 mr = 70567 m= 16861 mr = 40687 m= 3061 mr = 13512 m= 266 mr = 2198 m= 11 mr = 145 m= 0 mr = 3 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 44731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14680 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) : 1.661688 object centre at (A) : -12.34500 21.68200 28.08000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1812130 0.1875238 midg,1,midg; midg,igrid,midg 3.2097939E-02 -7.6033138E-02 1,midg,midg; igrid,midg,midg -2.9171787E-02 -1.3425368E-02 gauss-seidel spectral radius is 0.9990875 estimated iterations to convergence 262 setup time was (sec) 0.9600000 now iterating at: 11:01:22 rms-change max change #iterations 6.795518 298.1794 at 10iterations 3.700412 112.9520 at 20iterations 2.003279 60.86716 at 30iterations 1.082596 29.83172 at 40iterations 0.5869489 14.82496 at 50iterations 0.3155883 7.991652 at 60iterations 0.1712381 4.206961 at 70iterations 9.2118390E-02 2.341069 at 80iterations 4.9437795E-02 1.235260 at 90iterations 2.6721051E-02 0.6665859 at 100iterations 1.4366314E-02 0.3483810 at 110iterations 7.7651278E-03 0.2085075 at 120iterations 4.1716485E-03 0.1003046 at 130iterations 2.2544649E-03 6.2377930E-02 at 140iterations 1.2109528E-03 2.9357910E-02 at 150iterations 6.5145880E-04 1.4897823E-02 at 160iterations 3.5049583E-04 9.2182159E-03 at 170iterations 1.8922625E-04 4.5313835E-03 at 180iterations finished qdiffx linear iterations at : 11:01:34 total time elapsed so far: 13.66000 # loops : 180 mean,max change (kT/e) : 1.8922625E-04 4.5313835E-03 energy calculations done at 13.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 11:01:35 13.797u 0.355s 0:14.45 97.8% 0+0k 0+0io 0pf+0w