Tue Oct 11 08:20:19 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 Tue Oct 11 2011 at 08:20:19 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1152 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7430443 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): -6.467000 32.10100 ymin,ymax (A): 1.376000 40.08000 zmin,zma (A): -1.535000 46.37600 x,y,z range (A): 38.56800 38.70400 47.91100 scale (grids/A): 0.7430443 object centre (A): 12.81700 20.72800 22.42050 number of atom coordinates read : 1152 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 88.67268 89.35626 88.42636 assigned negative charge : -172.6512 centred at (gu) : 88.36953 89.30566 88.44006 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4315 nv = 96 ne = 84 npr = 22015 no. pairs analyzed = 22015 no. exposed pairs = 1517 no. arc points = 11011 no. surface atoms = 513 nbur = 639 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 298 mr = 2205 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.1200000 number of dielectric boundary points 2353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 927 ## 81 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4488 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5223910E-07 7.4456437E-08 midg,1,midg; midg,igrid,midg 8.6074323E-08 1.2060204E-07 1,midg,midg; igrid,midg,midg -9.8658731E-08 2.1676024E-07 gauss-seidel spectral radius is 0.9904633 estimated iterations to convergence 83 setup time was (sec) 0.3000000 now iterating at: 08:20:19 rms-change max change #iterations 0.1790678 27.85910 at 10iterations 2.3915712E-02 4.394287 at 20iterations 3.2287412E-03 0.6019783 at 30iterations 4.2839994E-04 7.5112581E-02 at 40iterations 5.5455435E-05 9.8648071E-03 at 50iterations finished qdiffx linear iterations at : 08:20:22 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.5455435E-05 9.8648071E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 08:20:22 3.316u 0.165s 0:03.80 91.3% 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 Tue Oct 11 2011 at 08:20:22 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1152 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.229133 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): -6.467000 32.10100 ymin,ymax (A): 1.376000 40.08000 zmin,zma (A): -1.535000 46.37600 x,y,z range (A): 38.56800 38.70400 47.91100 scale (grids/A): 2.229133 object centre (A): 12.81700 20.72800 22.42050 number of atom coordinates read : 1152 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 86.01813 88.06893 85.27908 assigned negative charge : -172.6512 centred at (gu) : 85.10878 87.91716 85.32043 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 45178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11011 grid for indexing accessible points = 1.400000 m= 17020 mr = 29276 m= 3291 mr = 12637 m= 324 mr = 2208 m= 13 mr = 178 m= 0 mr = 8 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 604 time to turn everything in is 0.2300000 number of dielectric boundary points 21519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8451 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) : 0.7430443 object centre at (A) : 12.81700 20.72800 22.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5377972E-02 1.0434950E-02 midg,1,midg; midg,igrid,midg 3.8351540E-02 3.6801960E-02 1,midg,midg; igrid,midg,midg -3.1923845E-02 3.9013453E-02 gauss-seidel spectral radius is 0.9988398 estimated iterations to convergence 232 setup time was (sec) 0.4400000 now iterating at: 08:20:23 rms-change max change #iterations 3.658242 208.2421 at 10iterations 1.812073 81.66206 at 20iterations 0.8992322 36.76253 at 30iterations 0.4482882 17.72047 at 40iterations 0.2203093 8.484299 at 50iterations 0.1093373 3.925050 at 60iterations 5.4043241E-02 2.084961 at 70iterations 2.6970021E-02 0.9878626 at 80iterations 1.3312222E-02 0.4969463 at 90iterations 6.5989550E-03 0.2455883 at 100iterations 3.2667343E-03 0.1400185 at 110iterations 1.6149117E-03 5.8608532E-02 at 120iterations finished qdiffx linear iterations at : 08:20:30 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.6149117E-03 5.8608532E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 08:20:30 7.443u 0.185s 0:07.92 96.2% 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 Tue Oct 11 2011 at 08:20:30 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1152 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.343699 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): -6.467000 32.10100 ymin,ymax (A): 1.376000 40.08000 zmin,zma (A): -1.535000 46.37600 x,y,z range (A): 38.56800 38.70400 47.91100 scale (grids/A): 3.343699 object centre (A): 12.81700 20.72800 22.42050 number of atom coordinates read : 1152 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 84.02724 87.10354 82.91858 assigned negative charge : -172.6512 centred at (gu) : 82.66322 86.87579 82.98073 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 103984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11011 grid for indexing accessible points = 1.400000 m= 52394 mr = 70792 m= 21564 mr = 42607 m= 6202 mr = 17806 m= 1266 mr = 4830 m= 202 mr = 977 m= 27 mr = 143 m= 0 mr = 23 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1963 time to turn everything in is 0.7000000 number of dielectric boundary points 48461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 8488 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) : 2.229133 object centre at (A) : 12.81700 20.72800 22.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2641234 0.1510648 midg,1,midg; midg,igrid,midg 0.3708486 0.3095314 1,midg,midg; igrid,midg,midg -0.2588454 0.2788622 gauss-seidel spectral radius is 0.9992966 estimated iterations to convergence 297 setup time was (sec) 0.9200000 now iterating at: 08:20:32 rms-change max change #iterations 8.057995 317.0936 at 10iterations 4.705951 134.9309 at 20iterations 2.736456 56.69463 at 30iterations 1.582729 39.38588 at 40iterations 0.9221518 20.27254 at 50iterations 0.5341155 11.87771 at 60iterations 0.3099732 6.864864 at 70iterations 0.1800951 3.988842 at 80iterations 0.1045231 2.247925 at 90iterations 6.0531013E-02 1.206244 at 100iterations 3.5160471E-02 0.7511277 at 110iterations 2.0388436E-02 0.4243584 at 120iterations 1.1873149E-02 0.2694073 at 130iterations 6.8793460E-03 0.1498260 at 140iterations 3.9907466E-03 8.1964493E-02 at 150iterations 2.3154861E-03 4.9139023E-02 at 160iterations 1.3475968E-03 3.0014038E-02 at 170iterations 7.8232458E-04 1.6975403E-02 at 180iterations finished qdiffx linear iterations at : 08:20:43 total time elapsed so far: 11.87000 # loops : 180 mean,max change (kT/e) : 7.8232458E-04 1.6975403E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 08:20:43 12.009u 0.214s 0:12.80 95.3% 0+0k 0+0io 0pf+0w