Sun Oct 9 22:42:34 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+sph2.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 = amb2.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 Sun Oct 9 2011 at 22:42:34 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6758808 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): -31.89400 20.44500 ymin,ymax (A): -2.263000 49.88800 zmin,zma (A): 15.15400 67.82600 x,y,z range (A): 52.33900 52.15100 52.67200 scale (grids/A): 0.6758808 object centre (A): -5.724501 23.81250 41.49000 number of atom coordinates read : 3036 total number of charged atoms : 2982 net assigned charge : 7.025017 assigned positive charge : 475.2898 centred at (gu) : 89.35606 90.98764 90.47084 assigned negative charge : -468.2661 centred at (gu) : 89.48310 91.11942 90.47504 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9709 nv = 96 ne = 84 npr = 56689 no. pairs analyzed = 56689 no. exposed pairs = 4144 no. arc points = 29925 no. surface atoms = 1370 nbur = 1666 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 668 mr = 5123 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 115 time to turn everything in is 0.3500000 number of dielectric boundary points 5148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2793 ## 287 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 11376 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6340858E-08 2.8415181E-08 midg,1,midg; midg,igrid,midg 6.0196996E-08 -2.4981457E-08 1,midg,midg; igrid,midg,midg 8.1974029E-08 -1.5796065E-08 gauss-seidel spectral radius is 0.9887083 estimated iterations to convergence 77 setup time was (sec) 0.5700000 now iterating at: 22:42:35 rms-change max change #iterations 0.2037540 25.87378 at 10iterations 2.2551434E-02 2.857868 at 20iterations 2.5221691E-03 0.3098526 at 30iterations 2.8465685E-04 3.2894135E-02 at 40iterations 3.3143326E-05 4.3869019E-03 at 50iterations finished qdiffx linear iterations at : 22:42:37 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 3.3143326E-05 4.3869019E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 22:42:38 3.360u 0.141s 0:03.86 90.6% 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 Sun Oct 9 2011 at 22:42:38 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.027642 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): -31.89400 20.44500 ymin,ymax (A): -2.263000 49.88800 zmin,zma (A): 15.15400 67.82600 x,y,z range (A): 52.33900 52.15100 52.67200 scale (grids/A): 2.027642 object centre (A): -5.724501 23.81250 41.49000 number of atom coordinates read : 3036 total number of charged atoms : 2982 net assigned charge : 7.025017 assigned positive charge : 475.2898 centred at (gu) : 88.06697 92.96191 91.41181 assigned negative charge : -468.2661 centred at (gu) : 88.44907 93.35777 91.42460 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 103389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29925 grid for indexing accessible points = 1.400000 m= 39931 mr = 69723 m= 7833 mr = 29014 m= 730 mr = 5037 m= 22 mr = 370 m= 0 mr = 2 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2685 time to turn everything in is 0.7400000 number of dielectric boundary points 47759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 23575 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) : 0.6758808 object centre at (A) : -5.724501 23.81250 41.49000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0997799E-03 9.1512501E-03 midg,1,midg; midg,igrid,midg 5.5730652E-02 6.0061540E-02 1,midg,midg; igrid,midg,midg 3.2883462E-02 8.9050140E-03 gauss-seidel spectral radius is 0.9988515 estimated iterations to convergence 234 setup time was (sec) 1.010000 now iterating at: 22:42:39 rms-change max change #iterations 5.342548 241.0737 at 10iterations 2.654079 77.23937 at 20iterations 1.314601 38.53210 at 30iterations 0.6552263 17.97808 at 40iterations 0.3262284 8.427607 at 50iterations 0.1620144 4.356628 at 60iterations 8.0497660E-02 2.236940 at 70iterations 4.0212393E-02 1.093582 at 80iterations 1.9974245E-02 0.6022882 at 90iterations 9.9367369E-03 0.2518632 at 100iterations 4.9564498E-03 0.1325459 at 110iterations 2.4699443E-03 6.7571640E-02 at 120iterations finished qdiffx linear iterations at : 22:42:46 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 2.4699443E-03 6.7571640E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 22:42:46 7.624u 0.173s 0:08.05 96.7% 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 Sun Oct 9 2011 at 22:42:46 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.041464 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): -31.89400 20.44500 ymin,ymax (A): -2.263000 49.88800 zmin,zma (A): 15.15400 67.82600 x,y,z range (A): 52.33900 52.15100 52.67200 scale (grids/A): 3.041464 object centre (A): -5.724501 23.81250 41.49000 number of atom coordinates read : 3036 total number of charged atoms : 2982 net assigned charge : 7.025017 assigned positive charge : 475.2898 centred at (gu) : 87.10032 94.44273 92.11750 assigned negative charge : -468.2661 centred at (gu) : 87.67354 95.03662 92.13657 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 238033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29925 grid for indexing accessible points = 1.400000 m= 124050 mr = 168854 m= 49891 mr = 100098 m= 14719 mr = 39799 m= 2968 mr = 11117 m= 319 mr = 2138 m= 5 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 8916 time to turn everything in is 1.960000 number of dielectric boundary points 107785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 23856 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) : 2.027642 object centre at (A) : -5.724501 23.81250 41.49000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6571870E-02 -5.2685000E-02 midg,1,midg; midg,igrid,midg 0.3592783 0.5728033 1,midg,midg; igrid,midg,midg 0.4909240 0.2879341 gauss-seidel spectral radius is 0.9993497 estimated iterations to convergence 309 setup time was (sec) 2.280000 now iterating at: 22:42:49 rms-change max change #iterations 12.38000 347.2681 at 10iterations 7.579435 154.0424 at 20iterations 4.602056 89.34364 at 30iterations 2.797392 53.23506 at 40iterations 1.689849 34.83331 at 50iterations 1.018807 19.00244 at 60iterations 0.6141078 12.03214 at 70iterations 0.3682182 6.131951 at 80iterations 0.2208897 4.037500 at 90iterations 0.1322373 2.311521 at 100iterations 7.9219855E-02 1.333296 at 110iterations 4.7325619E-02 0.7255921 at 120iterations 2.8251095E-02 0.4634018 at 130iterations 1.6900275E-02 0.2806969 at 140iterations 1.0099318E-02 0.1545525 at 150iterations 6.0220123E-03 9.2231750E-02 at 160iterations 3.5952078E-03 5.8206558E-02 at 170iterations 2.1413146E-03 3.2536745E-02 at 180iterations finished qdiffx linear iterations at : 22:42:59 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 2.1413146E-03 3.2536745E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 22:43:00 13.004u 0.155s 0:13.54 97.1% 0+0k 0+0io 0pf+0w