Wed Dec 21 14:22:05 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 21 2011 at 14:22:07 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 0.6013818 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): -23.75900 35.43800 ymin,ymax (A): -18.64500 20.54400 zmin,zma (A): -3.083000 38.59600 x,y,z range (A): 59.19700 39.18900 41.67900 scale (grids/A): 0.6013818 object centre (A): 5.839500 0.9494991 17.75650 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 2.000005 assigned positive charge : 285.5141 centred at (gu) : 89.59860 90.15945 90.24734 assigned negative charge : -283.5143 centred at (gu) : 89.61279 90.26297 90.40608 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4714 nv = 96 ne = 84 npr = 40037 no. pairs analyzed = 40037 no. exposed pairs = 2422 no. arc points = 17054 no. surface atoms = 820 nbur = 1126 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 196 mr = 2556 m= 0 mr = 8 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3500000 number of dielectric boundary points 2346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1707 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 5783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9670166E-09 -3.7959391E-09 midg,1,midg; midg,igrid,midg 3.6304562E-09 -2.0749782E-09 1,midg,midg; igrid,midg,midg 1.4349661E-09 4.7984994E-10 gauss-seidel spectral radius is 0.9856334 estimated iterations to convergence 68 setup time was (sec) 0.8000000 now iterating at: 14:22:09 rms-change max change #iterations 9.3714081E-02 20.13143 at 10iterations 8.1639439E-03 1.335006 at 20iterations 6.7235989E-04 0.1044998 at 30iterations 5.8670110E-05 1.0734558E-02 at 40iterations 4.8841566E-06 8.9883804E-04 at 50iterations finished qdiffx linear iterations at : 14:22:15 total time elapsed so far: 7.630000 # loops : 50 mean,max change (kT/e) : 4.8841566E-06 8.9883804E-04 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 14:22:21 7.847u 0.645s 0:15.38 55.1% 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 21 2011 at 14:22:24 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 1.804146 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): -23.75900 35.43800 ymin,ymax (A): -18.64500 20.54400 zmin,zma (A): -3.083000 38.59600 x,y,z range (A): 59.19700 39.18900 41.67900 scale (grids/A): 1.804146 object centre (A): 5.839500 0.9494991 17.75650 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 2.000005 assigned positive charge : 285.5141 centred at (gu) : 88.79593 90.47845 90.74192 assigned negative charge : -283.5143 centred at (gu) : 88.83855 90.78906 91.21851 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 51718 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17054 grid for indexing accessible points = 1.400000 m= 18033 mr = 35566 m= 2221 mr = 13427 m= 73 mr = 1362 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2026 time to turn everything in is 0.5200000 number of dielectric boundary points 21685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14173 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) : 0.6013818 object centre at (A) : 5.839500 0.9494991 17.75650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5689902E-03 -6.9476473E-03 midg,1,midg; midg,igrid,midg 1.8699234E-03 -5.5270460E-03 1,midg,midg; igrid,midg,midg 3.8329292E-02 3.1726174E-02 gauss-seidel spectral radius is 0.9984015 estimated iterations to convergence 198 setup time was (sec) 0.8600000 now iterating at: 14:22:26 rms-change max change #iterations 3.206387 158.6646 at 10iterations 1.403495 62.43651 at 20iterations 0.6203937 28.23313 at 30iterations 0.2725020 10.25252 at 40iterations 0.1197846 4.646378 at 50iterations 5.2630767E-02 2.070617 at 60iterations 2.3138246E-02 0.9972401 at 70iterations 1.0174653E-02 0.3922348 at 80iterations 4.4770781E-03 0.1675048 at 90iterations 1.9705428E-03 8.3126068E-02 at 100iterations 8.6368126E-04 3.3020020E-02 at 110iterations 3.8041006E-04 1.4770508E-02 at 120iterations finished qdiffx linear iterations at : 14:22:40 total time elapsed so far: 14.89000 # loops : 120 mean,max change (kT/e) : 3.8041006E-04 1.4770508E-02 energy calculations done at 14.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.12000 DelPhi exited at 14:22:42 15.121u 0.504s 0:18.41 84.8% 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 Wed Dec 21 2011 at 14:22:42 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 2.706218 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): -23.75900 35.43800 ymin,ymax (A): -18.64500 20.54400 zmin,zma (A): -3.083000 38.59600 x,y,z range (A): 59.19700 39.18900 41.67900 scale (grids/A): 2.706218 object centre (A): 5.839500 0.9494991 17.75650 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 2.000005 assigned positive charge : 285.5141 centred at (gu) : 88.19373 90.71777 91.11298 assigned negative charge : -283.5143 centred at (gu) : 88.25800 91.18369 91.82777 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 119627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17054 grid for indexing accessible points = 1.400000 m= 59507 mr = 86024 m= 19726 mr = 49102 m= 3843 mr = 15943 m= 275 mr = 2917 m= 10 mr = 126 m= 0 mr = 1 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 6858 time to turn everything in is 1.500000 number of dielectric boundary points 48875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 14512 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) : 1.804146 object centre at (A) : 5.839500 0.9494991 17.75650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3942602E-02 -5.8924593E-02 midg,1,midg; midg,igrid,midg 8.6638620E-03 -4.6795525E-02 1,midg,midg; igrid,midg,midg 0.4570601 0.3264827 gauss-seidel spectral radius is 0.9991747 estimated iterations to convergence 275 setup time was (sec) 2.020000 now iterating at: 14:22:45 rms-change max change #iterations 7.677495 293.4314 at 10iterations 4.295216 110.3442 at 20iterations 2.397231 55.79171 at 30iterations 1.333479 33.76699 at 40iterations 0.7415645 18.20263 at 50iterations 0.4120754 10.83525 at 60iterations 0.2289208 5.463448 at 70iterations 0.1271675 2.820245 at 80iterations 7.0536003E-02 1.527406 at 90iterations 3.9235499E-02 0.8219366 at 100iterations 2.1804817E-02 0.4514167 at 110iterations 1.2101131E-02 0.2557487 at 120iterations 6.7229206E-03 0.1556225 at 130iterations 3.7231371E-03 8.0309868E-02 at 140iterations 2.0734610E-03 4.4683456E-02 at 150iterations 1.1522848E-03 2.4788857E-02 at 160iterations 6.3953915E-04 1.5304565E-02 at 170iterations 3.5478009E-04 7.6518059E-03 at 180iterations finished qdiffx linear iterations at : 14:23:02 total time elapsed so far: 19.30000 # loops : 180 mean,max change (kT/e) : 3.5478009E-04 7.6518059E-03 energy calculations done at 19.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.51000 DelPhi exited at 14:23:05 19.517u 0.740s 0:23.09 87.7% 0+0k 0+0io 0pf+0w