Wed Dec 21 14:20:48 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 14:20:48 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1895 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 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: 0.6122519 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): -9.025000 49.12100 ymin,ymax (A): 8.556001 47.80500 zmin,zma (A): -3.603000 38.92000 x,y,z range (A): 58.14600 39.24900 42.52300 scale (grids/A): 0.6122519 object centre (A): 20.04800 28.18050 17.65850 number of atom coordinates read : 1895 total number of charged atoms : 1763 net assigned charge : -3.799990 assigned positive charge : 275.1901 centred at (gu) : 90.25948 89.73610 90.52266 assigned negative charge : -278.9903 centred at (gu) : 90.27682 89.65852 90.62071 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4857 nv = 96 ne = 84 npr = 38747 no. pairs analyzed = 38747 no. exposed pairs = 2371 no. arc points = 16481 no. surface atoms = 808 nbur = 1087 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 212 mr = 2685 m= 0 mr = 12 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.1500000 number of dielectric boundary points 2372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1637 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2100000 number of grid points assigned charge 5804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1585167E-09 -6.9062112E-09 midg,1,midg; midg,igrid,midg -5.6734355E-09 5.1552201E-10 1,midg,midg; igrid,midg,midg -1.6218122E-09 -3.2099723E-09 gauss-seidel spectral radius is 0.9861296 estimated iterations to convergence 70 setup time was (sec) 0.3500000 now iterating at: 14:20:49 rms-change max change #iterations 9.9955052E-02 20.08646 at 10iterations 8.7723471E-03 1.575396 at 20iterations 8.0710277E-04 0.1408005 at 30iterations 6.9339141E-05 1.1871338E-02 at 40iterations 6.2026816E-06 1.0234714E-03 at 50iterations finished qdiffx linear iterations at : 14:20:52 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 6.2026816E-06 1.0234714E-03 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:20:53 3.765u 0.198s 0:04.24 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 Wed Dec 21 2011 at 14:20:53 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1895 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 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: 1.836756 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): -9.025000 49.12100 ymin,ymax (A): 8.556001 47.80500 zmin,zma (A): -3.603000 38.92000 x,y,z range (A): 58.14600 39.24900 42.52300 scale (grids/A): 1.836756 object centre (A): 20.04800 28.18050 17.65850 number of atom coordinates read : 1895 total number of charged atoms : 1763 net assigned charge : -3.799990 assigned positive charge : 275.1901 centred at (gu) : 90.77831 89.20822 91.56801 assigned negative charge : -278.9903 centred at (gu) : 90.83079 88.97595 91.86231 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 52994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16481 grid for indexing accessible points = 1.400000 m= 17961 mr = 36629 m= 2181 mr = 13320 m= 84 mr = 1271 m= 4 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1491 time to turn everything in is 0.2700000 number of dielectric boundary points 21986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 13836 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) : 0.6122519 object centre at (A) : 20.04800 28.18050 17.65850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6813340E-03 -1.3925771E-02 midg,1,midg; midg,igrid,midg -2.6739743E-03 7.5507554E-04 1,midg,midg; igrid,midg,midg 1.2104008E-03 1.5354920E-02 gauss-seidel spectral radius is 0.9984522 estimated iterations to convergence 202 setup time was (sec) 0.5000000 now iterating at: 14:20:53 rms-change max change #iterations 3.259882 156.3469 at 10iterations 1.446769 60.02589 at 20iterations 0.6433065 23.58587 at 30iterations 0.2879112 10.97038 at 40iterations 0.1283541 4.701988 at 50iterations 5.7107277E-02 2.083998 at 60iterations 2.5348946E-02 1.049507 at 70iterations 1.1358446E-02 0.4217606 at 80iterations 5.0756675E-03 0.2009125 at 90iterations 2.2595827E-03 8.2935333E-02 at 100iterations 1.0057023E-03 3.5600662E-02 at 110iterations 4.4913581E-04 1.6277313E-02 at 120iterations finished qdiffx linear iterations at : 14:21:01 total time elapsed so far: 8.400000 # loops : 120 mean,max change (kT/e) : 4.4913581E-04 1.6277313E-02 energy calculations done at 8.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.510000 DelPhi exited at 14:21:02 8.513u 0.263s 0:09.40 93.2% 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 14:21:02 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1895 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 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: 2.755133 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): -9.025000 49.12100 ymin,ymax (A): 8.556001 47.80500 zmin,zma (A): -3.603000 38.92000 x,y,z range (A): 58.14600 39.24900 42.52300 scale (grids/A): 2.755133 object centre (A): 20.04800 28.18050 17.65850 number of atom coordinates read : 1895 total number of charged atoms : 1763 net assigned charge : -3.799990 assigned positive charge : 275.1901 centred at (gu) : 91.16764 88.81226 92.35212 assigned negative charge : -278.9903 centred at (gu) : 91.24632 88.46394 92.79356 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 122669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16481 grid for indexing accessible points = 1.400000 m= 60063 mr = 88752 m= 19472 mr = 49454 m= 3738 mr = 15676 m= 361 mr = 2648 m= 18 mr = 201 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 5032 time to turn everything in is 0.7400000 number of dielectric boundary points 49590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 14103 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) : 1.836756 object centre at (A) : 20.04800 28.18050 17.65850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2507798E-03 -0.1399732 midg,1,midg; midg,igrid,midg 8.6233988E-03 8.3009843E-03 1,midg,midg; igrid,midg,midg 7.4274063E-02 0.2725995 gauss-seidel spectral radius is 0.9991884 estimated iterations to convergence 277 setup time was (sec) 0.9700000 now iterating at: 14:21:03 rms-change max change #iterations 7.835825 287.2869 at 10iterations 4.445305 113.5666 at 20iterations 2.506285 67.81494 at 30iterations 1.406529 31.30731 at 40iterations 0.7888504 18.10091 at 50iterations 0.4414210 9.929103 at 60iterations 0.2468822 5.853210 at 70iterations 0.1379633 3.217367 at 80iterations 7.7121943E-02 1.892120 at 90iterations 4.3138985E-02 0.9751740 at 100iterations 2.4068905E-02 0.5122223 at 110iterations 1.3455521E-02 0.2842426 at 120iterations 7.5328471E-03 0.1571627 at 130iterations 4.1963244E-03 9.5860720E-02 at 140iterations 2.3466696E-03 5.0485611E-02 at 150iterations 1.3117344E-03 2.6196480E-02 at 160iterations 7.3137804E-04 1.4666557E-02 at 170iterations 4.0913848E-04 8.2681179E-03 at 180iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 13.66000 # loops : 180 mean,max change (kT/e) : 4.0913848E-04 8.2681179E-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 14:21:20 13.797u 0.415s 0:18.19 78.0% 0+0k 0+0io 0pf+0w