Wed Feb 15 08:56:17 PST 2012 #!/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_thinner.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 Feb 15 2012 at 08:56:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 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: 0.5636925 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): 60.12300 113.6320 ymin,ymax (A): -7.224000 55.93100 zmin,zma (A): -26.15100 30.11800 x,y,z range (A): 53.50901 63.15500 56.26900 scale (grids/A): 0.5636925 object centre (A): 86.87750 24.35350 1.983500 number of atom coordinates read : 2726 total number of charged atoms : 2583 net assigned charge : -2.999984 assigned positive charge : 393.0180 centred at (gu) : 89.90332 89.86395 90.04644 assigned negative charge : -396.0197 centred at (gu) : 89.97508 89.66365 90.15456 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5964 nv = 96 ne = 84 npr = 53137 no. pairs analyzed = 53137 no. exposed pairs = 4261 no. arc points = 30759 no. surface atoms = 1399 nbur = 1327 mkacc time = 0.1200000 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 = 1.512000 m= 283 mr = 2483 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2970 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7470 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3181328E-10 -1.6106976E-09 midg,1,midg; midg,igrid,midg -2.7600067E-09 1.7798606E-09 1,midg,midg; igrid,midg,midg 4.5216494E-10 -1.1472782E-09 gauss-seidel spectral radius is 0.9837697 estimated iterations to convergence 65 setup time was (sec) 0.5400000 now iterating at: 08:56:18 rms-change max change #iterations 7.6379105E-02 11.79013 at 10iterations 5.6134285E-03 1.001143 at 20iterations 4.5924992E-04 8.0059052E-02 at 30iterations 6.4988577E-05 1.2770653E-02 at 40iterations 1.4496582E-05 3.1347275E-03 at 50iterations finished qdiffx linear iterations at : 08:56:21 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.4496582E-05 3.1347275E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:56:21 3.387u 0.168s 0:04.00 88.5% 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 Wed Feb 15 2012 at 08:56:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 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: 1.691078 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): 60.12300 113.6320 ymin,ymax (A): -7.224000 55.93100 zmin,zma (A): -26.15100 30.11800 x,y,z range (A): 53.50901 63.15500 56.26900 scale (grids/A): 1.691078 object centre (A): 86.87750 24.35350 1.983500 number of atom coordinates read : 2726 total number of charged atoms : 2583 net assigned charge : -2.999984 assigned positive charge : 393.0180 centred at (gu) : 89.70904 89.59115 90.13826 assigned negative charge : -396.0197 centred at (gu) : 89.92514 88.99070 90.46344 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 63797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30759 grid for indexing accessible points = 1.400000 m= 19493 mr = 37941 m= 2531 mr = 11954 m= 99 mr = 1172 m= 0 mr = 10 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 34843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 20007 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) : 0.5636925 object centre at (A) : 86.87750 24.35350 1.983500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1355471E-04 -1.2322032E-02 midg,1,midg; midg,igrid,midg -2.2836540E-02 -1.0516590E-02 1,midg,midg; igrid,midg,midg 7.6473276E-03 -5.4060726E-04 gauss-seidel spectral radius is 0.9983356 estimated iterations to convergence 195 setup time was (sec) 0.8200000 now iterating at: 08:56:23 rms-change max change #iterations 3.376209 162.6760 at 10iterations 1.450025 53.17050 at 20iterations 0.6244938 26.91570 at 30iterations 0.2683267 9.940056 at 40iterations 0.1159222 4.882097 at 50iterations 4.9969714E-02 1.730579 at 60iterations 2.1564990E-02 0.7797356 at 70iterations 9.3156016E-03 0.3339558 at 80iterations 4.0451153E-03 0.1431484 at 90iterations 1.7549729E-03 6.1717987E-02 at 100iterations 7.6769403E-04 2.8404236E-02 at 110iterations 3.3827638E-04 1.3196945E-02 at 120iterations finished qdiffx linear iterations at : 08:56:30 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 3.3827638E-04 1.3196945E-02 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 08:56:31 8.304u 0.265s 0:09.52 89.9% 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 Wed Feb 15 2012 at 08:56:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 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: 2.536616 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): 60.12300 113.6320 ymin,ymax (A): -7.224000 55.93100 zmin,zma (A): -26.15100 30.11800 x,y,z range (A): 53.50901 63.15500 56.26900 scale (grids/A): 2.536616 object centre (A): 86.87750 24.35350 1.983500 number of atom coordinates read : 2726 total number of charged atoms : 2583 net assigned charge : -2.999984 assigned positive charge : 393.0180 centred at (gu) : 89.56326 89.38644 90.20734 assigned negative charge : -396.0197 centred at (gu) : 89.88753 88.48602 90.69501 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 147912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30759 grid for indexing accessible points = 1.400000 m= 64162 mr = 94979 m= 20148 mr = 46292 m= 4019 mr = 14063 m= 368 mr = 2516 m= 6 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 78615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 20654 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) : 1.691078 object centre at (A) : 86.87750 24.35350 1.983500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7757955E-02 -0.1678452 midg,1,midg; midg,igrid,midg -0.2765037 -0.1477027 1,midg,midg; igrid,midg,midg 0.1375001 -1.7574253E-02 gauss-seidel spectral radius is 0.9992068 estimated iterations to convergence 280 setup time was (sec) 1.520000 now iterating at: 08:56:33 rms-change max change #iterations 8.743234 269.4749 at 10iterations 5.127546 138.8051 at 20iterations 2.983869 84.69229 at 30iterations 1.716756 48.65194 at 40iterations 0.9873891 25.72991 at 50iterations 0.5641130 12.57521 at 60iterations 0.3214743 7.151299 at 70iterations 0.1824822 3.997594 at 80iterations 0.1033378 2.235600 at 90iterations 5.8541235E-02 1.274847 at 100iterations 3.3203624E-02 0.6881549 at 110iterations 1.8757723E-02 0.4476013 at 120iterations 1.0589912E-02 0.2379556 at 130iterations 5.9789070E-03 0.1403942 at 140iterations 3.3739023E-03 6.4369202E-02 at 150iterations 1.9045043E-03 3.8837433E-02 at 160iterations 1.0749571E-03 2.3941040E-02 at 170iterations 6.0745154E-04 1.2346268E-02 at 180iterations finished qdiffx linear iterations at : 08:56:44 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 6.0745154E-04 1.2346268E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 08:56:45 13.105u 0.204s 0:13.64 97.5% 0+0k 0+0io 0pf+0w