Sun Oct 9 15:32:22 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 15:32:22 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5705 !!! WARNING: HIQ 148 has a net charge of 0.5140 !!! WARNING: HIR 541 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5084915 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): 154.2930 224.3040 ymin,ymax (A): 91.20400 154.4660 zmin,zma (A): -0.7020000 67.74800 x,y,z range (A): 70.01100 63.26200 68.45000 scale (grids/A): 0.5084915 object centre (A): 189.2985 122.8350 33.52300 number of atom coordinates read : 5705 total number of charged atoms : 5534 net assigned charge : -1.471967 assigned positive charge : 874.6912 centred at (gu) : 89.85632 89.17699 89.74514 assigned negative charge : -876.1709 centred at (gu) : 89.92023 89.22726 89.64069 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9031 nv = 96 ne = 84 npr = 117958 no. pairs analyzed = 117958 no. exposed pairs = 6586 no. arc points = 45224 no. surface atoms = 2196 nbur = 3509 mkacc time = 0.2000000 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 = 1.680000 m= 272 mr = 4967 m= 0 mr = 3 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3700000 number of dielectric boundary points 4333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4339 ## 629 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 12264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5080272E-10 2.6132679E-10 midg,1,midg; midg,igrid,midg 1.5702518E-10 -1.3393195E-10 1,midg,midg; igrid,midg,midg 1.7114418E-10 -1.9921767E-10 gauss-seidel spectral radius is 0.9802738 estimated iterations to convergence 59 setup time was (sec) 0.5500000 now iterating at: 15:32:23 rms-change max change #iterations 7.3819265E-02 12.19220 at 10iterations 4.7545508E-03 0.7295418 at 20iterations 6.7274144E-04 0.1008911 at 30iterations 1.7174819E-04 2.3593903E-02 at 40iterations 5.0000250E-05 6.0138702E-03 at 50iterations finished qdiffx linear iterations at : 15:32:26 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 5.0000250E-05 6.0138702E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 15:32:27 3.628u 0.204s 0:04.10 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 Sun Oct 9 2011 at 15:32:27 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5705 !!! WARNING: HIQ 148 has a net charge of 0.5140 !!! WARNING: HIR 541 has a net charge of 0.5140 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: 1.525475 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): 154.2930 224.3040 ymin,ymax (A): 91.20400 154.4660 zmin,zma (A): -0.7020000 67.74800 x,y,z range (A): 70.01100 63.26200 68.45000 scale (grids/A): 1.525475 object centre (A): 189.2985 122.8350 33.52300 number of atom coordinates read : 5705 total number of charged atoms : 5534 net assigned charge : -1.471967 assigned positive charge : 874.6912 centred at (gu) : 89.56721 87.52929 89.23393 assigned negative charge : -876.1709 centred at (gu) : 89.76046 87.68156 88.92216 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 103303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45224 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29362 mr = 73455 m= 2530 mr = 20138 m= 47 mr = 1128 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 4770 time to turn everything in is 0.5000000 number of dielectric boundary points 40521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 578 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 41452 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) : 0.5084915 object centre at (A) : 189.2985 122.8350 33.52300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0392588E-03 2.5580642E-03 midg,1,midg; midg,igrid,midg 5.1582465E-03 -3.2513142E-03 1,midg,midg; igrid,midg,midg -1.7626623E-02 -7.6182769E-03 gauss-seidel spectral radius is 0.9981599 estimated iterations to convergence 185 setup time was (sec) 0.7500000 now iterating at: 15:32:27 rms-change max change #iterations 4.218428 155.5613 at 10iterations 1.753112 54.40029 at 20iterations 0.7270329 20.53235 at 30iterations 0.3023286 9.669759 at 40iterations 0.1257937 3.676630 at 50iterations 5.2473966E-02 1.533730 at 60iterations 2.1830162E-02 0.6340046 at 70iterations 9.1020083E-03 0.2957611 at 80iterations 3.8104965E-03 0.1169014 at 90iterations 1.6148345E-03 4.6108246E-02 at 100iterations 6.9334178E-04 2.1400452E-02 at 110iterations 3.0989092E-04 8.9759827E-03 at 120iterations finished qdiffx linear iterations at : 15:32:35 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 3.0989092E-04 8.9759827E-03 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 15:32:35 8.226u 0.204s 0:08.81 95.5% 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 15:32:35 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5705 !!! WARNING: HIQ 148 has a net charge of 0.5140 !!! WARNING: HIR 541 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.288212 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): 154.2930 224.3040 ymin,ymax (A): 91.20400 154.4660 zmin,zma (A): -0.7020000 67.74800 x,y,z range (A): 70.01100 63.26200 68.45000 scale (grids/A): 2.288212 object centre (A): 189.2985 122.8350 33.52300 number of atom coordinates read : 5705 total number of charged atoms : 5534 net assigned charge : -1.471967 assigned positive charge : 874.6912 centred at (gu) : 89.35038 86.29382 88.85039 assigned negative charge : -876.1709 centred at (gu) : 89.64048 86.52233 88.38313 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 241623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45224 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 107217 mr = 180235 m= 26515 mr = 85338 m= 3518 mr = 19627 m= 169 mr = 2161 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 15866 time to turn everything in is 1.220000 number of dielectric boundary points 91615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 44152 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) : 1.525475 object centre at (A) : 189.2985 122.8350 33.52300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1390591 -3.0715059E-02 midg,1,midg; midg,igrid,midg 0.1239947 -7.7897891E-02 1,midg,midg; igrid,midg,midg -0.3956937 -0.1239214 gauss-seidel spectral radius is 0.9991890 estimated iterations to convergence 277 setup time was (sec) 1.490000 now iterating at: 15:32:37 rms-change max change #iterations 11.36461 297.2137 at 10iterations 6.560199 141.9216 at 20iterations 3.748035 105.0267 at 30iterations 2.135707 43.62986 at 40iterations 1.210890 23.78551 at 50iterations 0.6859229 13.39492 at 60iterations 0.3870935 7.425400 at 70iterations 0.2184143 4.724564 at 80iterations 0.1228708 2.454605 at 90iterations 6.9194928E-02 1.167397 at 100iterations 3.8884591E-02 0.6560745 at 110iterations 2.1868702E-02 0.4214878 at 120iterations 1.2265394E-02 0.2335281 at 130iterations 6.8851202E-03 0.1333027 at 140iterations 3.8653582E-03 6.1371565E-02 at 150iterations 2.1730356E-03 3.7781715E-02 at 160iterations 1.2208691E-03 2.1516800E-02 at 170iterations 6.8594812E-04 1.1548996E-02 at 180iterations finished qdiffx linear iterations at : 15:32:49 total time elapsed so far: 13.58000 # loops : 180 mean,max change (kT/e) : 6.8594812E-04 1.1548996E-02 energy calculations done at 13.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.73000 DelPhi exited at 15:32:50 13.728u 0.231s 0:14.24 97.9% 0+0k 0+0io 0pf+0w