Sun Oct 9 19:12:17 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 19:12:17 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5120 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: HIR 571 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5214818 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): 3.340000 68.25800 ymin,ymax (A): -8.875999 59.39100 zmin,zma (A): -2.260000 61.93800 x,y,z range (A): 64.91801 68.26700 64.19800 scale (grids/A): 0.5214818 object centre (A): 35.79900 25.25750 29.83900 number of atom coordinates read : 5120 total number of charged atoms : 4960 net assigned charge : 1.268044 assigned positive charge : 788.6609 centred at (gu) : 87.76051 88.18789 89.25319 assigned negative charge : -787.3987 centred at (gu) : 87.64496 88.21016 89.24535 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8924 nv = 96 ne = 84 npr = 103453 no. pairs analyzed = 103453 no. exposed pairs = 6048 no. arc points = 40331 no. surface atoms = 2068 nbur = 3052 mkacc time = 0.2300000 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 = 1.652000 m= 353 mr = 4995 m= 0 mr = 15 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4075 ## 544 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11935 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9538429E-12 6.1851371E-11 midg,1,midg; midg,igrid,midg 2.2380718E-10 -3.6746006E-11 1,midg,midg; igrid,midg,midg -8.7747026E-10 3.0682720E-10 gauss-seidel spectral radius is 0.9812096 estimated iterations to convergence 60 setup time was (sec) 0.7500000 now iterating at: 19:12:18 rms-change max change #iterations 8.4730789E-02 11.82795 at 10iterations 1.0767700E-02 1.602814 at 20iterations 4.4305068E-03 0.6664886 at 30iterations 2.1024861E-03 0.3123589 at 40iterations 1.0140900E-03 0.1465111 at 50iterations finished qdiffx linear iterations at : 19:12:21 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 1.0140900E-03 0.1465111 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 19:12:22 4.431u 0.253s 0:04.95 94.5% 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 Sun Oct 9 2011 at 19:12:22 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5120 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: HIR 571 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.564445 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): 3.340000 68.25800 ymin,ymax (A): -8.875999 59.39100 zmin,zma (A): -2.260000 61.93800 x,y,z range (A): 64.91801 68.26700 64.19800 scale (grids/A): 1.564445 object centre (A): 35.79900 25.25750 29.83900 number of atom coordinates read : 5120 total number of charged atoms : 4960 net assigned charge : 1.268044 assigned positive charge : 788.6609 centred at (gu) : 83.27975 84.56195 87.75817 assigned negative charge : -787.3987 centred at (gu) : 82.93481 84.63049 87.73624 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 101930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40331 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 32778 mr = 73724 m= 3290 mr = 22921 m= 77 mr = 1606 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 39822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 483 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 37511 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) : 0.5214818 object centre at (A) : 35.79900 25.25750 29.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4220098E-03 -1.3893786E-02 midg,1,midg; midg,igrid,midg 1.8189831E-02 -1.5101511E-03 1,midg,midg; igrid,midg,midg -1.3423290E-02 7.2442531E-03 gauss-seidel spectral radius is 0.9982128 estimated iterations to convergence 188 setup time was (sec) 1.060000 now iterating at: 19:12:23 rms-change max change #iterations 4.240489 140.7201 at 10iterations 1.781965 55.28190 at 20iterations 0.7503123 21.76012 at 30iterations 0.3169330 9.591967 at 40iterations 0.1343332 3.952442 at 50iterations 5.7832457E-02 1.686844 at 60iterations 2.5995376E-02 0.7732506 at 70iterations 1.2866815E-02 0.4104500 at 80iterations 7.5185867E-03 0.2575684 at 90iterations 5.0661424E-03 0.1612015 at 100iterations 3.7103044E-03 0.1173038 at 110iterations 2.7975452E-03 8.6135864E-02 at 120iterations finished qdiffx linear iterations at : 19:12:32 total time elapsed so far: 10.02000 # loops : 120 mean,max change (kT/e) : 2.7975452E-03 8.6135864E-02 energy calculations done at 10.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.19000 DelPhi exited at 19:12:33 10.197u 0.313s 0:10.83 96.9% 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 19:12:33 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5120 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: HIR 571 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.346668 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): 3.340000 68.25800 ymin,ymax (A): -8.875999 59.39100 zmin,zma (A): -2.260000 61.93800 x,y,z range (A): 64.91801 68.26700 64.19800 scale (grids/A): 2.346668 object centre (A): 35.79900 25.25750 29.83900 number of atom coordinates read : 5120 total number of charged atoms : 4960 net assigned charge : 1.268044 assigned positive charge : 788.6609 centred at (gu) : 79.91929 81.84240 86.63690 assigned negative charge : -787.3987 centred at (gu) : 79.40212 81.94576 86.60444 start vw surface at 0.2000000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 237450 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40331 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 114729 mr = 179776 m= 32109 mr = 92534 m= 5043 mr = 24139 m= 294 mr = 3243 m= 5 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 89810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 39574 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) : 1.564445 object centre at (A) : 35.79900 25.25750 29.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1622909 -0.3509356 midg,1,midg; midg,igrid,midg 9.6827433E-02 -5.1661585E-02 1,midg,midg; igrid,midg,midg -0.2632626 5.9892733E-02 gauss-seidel spectral radius is 0.9991872 estimated iterations to convergence 277 setup time was (sec) 2.310000 now iterating at: 19:12:35 rms-change max change #iterations 11.22638 365.8500 at 10iterations 6.486128 133.8115 at 20iterations 3.721415 73.99000 at 30iterations 2.116143 43.62745 at 40iterations 1.200993 23.21046 at 50iterations 0.6801208 13.73943 at 60iterations 0.3845917 7.183460 at 70iterations 0.2174038 3.848507 at 80iterations 0.1228500 2.120407 at 90iterations 6.9407322E-02 1.217028 at 100iterations 3.9620783E-02 0.7111511 at 110iterations 2.2973668E-02 0.4089813 at 120iterations 1.3827154E-02 0.2920723 at 130iterations 8.8044060E-03 0.1884613 at 140iterations 6.0279253E-03 0.1147156 at 150iterations 4.4749393E-03 8.9065552E-02 at 160iterations 3.5149755E-03 6.1916351E-02 at 170iterations 2.8604411E-03 5.1097870E-02 at 180iterations finished qdiffx linear iterations at : 19:12:51 total time elapsed so far: 17.83000 # loops : 180 mean,max change (kT/e) : 2.8604411E-03 5.1097870E-02 energy calculations done at 17.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.01000 DelPhi exited at 19:12:51 18.012u 0.379s 0:18.86 97.4% 0+0k 0+0io 0pf+0w