Tue Oct 11 03:15:06 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+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 Tue Oct 11 2011 at 03:15:07 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 = 3525 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: 0.5335091 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): -38.47200 21.33000 ymin,ymax (A): -7.707000 46.39600 zmin,zma (A): -70.59200 -3.864000 x,y,z range (A): 59.80200 54.10300 66.72800 scale (grids/A): 0.5335091 object centre (A): -8.571000 19.34450 -37.22800 number of atom coordinates read : 3525 total number of charged atoms : 3384 net assigned charge : -7.499971 assigned positive charge : 536.6349 centred at (gu) : 92.10487 91.12173 92.33725 assigned negative charge : -544.1368 centred at (gu) : 92.09972 91.09506 92.35175 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6446 nv = 96 ne = 84 npr = 71065 no. pairs analyzed = 71065 no. exposed pairs = 4572 no. arc points = 32049 no. surface atoms = 1519 nbur = 2006 mkacc time = 0.1500000 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 = 1.624000 m= 254 mr = 3251 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3289 ## 453 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8624 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1910319E-10 -6.3333366E-10 midg,1,midg; midg,igrid,midg -3.1278638E-10 -1.9240087E-10 1,midg,midg; igrid,midg,midg -1.8298789E-10 -4.2769480E-10 gauss-seidel spectral radius is 0.9819361 estimated iterations to convergence 61 setup time was (sec) 0.5600000 now iterating at: 03:15:07 rms-change max change #iterations 7.4628942E-02 12.88481 at 10iterations 4.8326575E-03 0.7837477 at 20iterations 5.5397593E-04 7.2679520E-02 at 30iterations 1.4043164E-04 1.9108772E-02 at 40iterations 4.1932428E-05 5.7086945E-03 at 50iterations finished qdiffx linear iterations at : 03:15:10 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 4.1932428E-05 5.7086945E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 03:15:10 3.234u 0.182s 0:03.74 91.1% 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 Tue Oct 11 2011 at 03:15:10 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 = 3525 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: 1.600527 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): -38.47200 21.33000 ymin,ymax (A): -7.707000 46.39600 zmin,zma (A): -70.59200 -3.864000 x,y,z range (A): 59.80200 54.10300 66.72800 scale (grids/A): 1.600527 object centre (A): -8.571000 19.34450 -37.22800 number of atom coordinates read : 3525 total number of charged atoms : 3384 net assigned charge : -7.499971 assigned positive charge : 536.6349 centred at (gu) : 96.31368 93.36439 97.01086 assigned negative charge : -544.1368 centred at (gu) : 96.29882 93.28491 97.05482 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 71606 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32049 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21866 mr = 48249 m= 2046 mr = 14473 m= 54 mr = 909 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 31939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 458 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 25746 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) : 0.5335091 object centre at (A) : -8.571000 19.34450 -37.22800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5014615E-02 -1.7459767E-02 midg,1,midg; midg,igrid,midg -2.4283710E-03 -2.8032907E-03 1,midg,midg; igrid,midg,midg -3.2401632E-03 -2.3104101E-03 gauss-seidel spectral radius is 0.9981566 estimated iterations to convergence 185 setup time was (sec) 0.8100000 now iterating at: 03:15:11 rms-change max change #iterations 3.518553 165.3205 at 10iterations 1.451658 57.73844 at 20iterations 0.6021434 22.70974 at 30iterations 0.2483190 8.798326 at 40iterations 0.1028793 4.420074 at 50iterations 4.2673610E-02 1.454487 at 60iterations 1.7660206E-02 0.5972075 at 70iterations 7.4045011E-03 0.2684937 at 80iterations 3.1350011E-03 0.1151326 at 90iterations 1.3524515E-03 4.6836853E-02 at 100iterations 6.1613589E-04 2.0633698E-02 at 110iterations 3.0584185E-04 1.0750771E-02 at 120iterations finished qdiffx linear iterations at : 03:15:18 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 3.0584185E-04 1.0750771E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 03:15:18 7.353u 0.226s 0:07.91 95.7% 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 03:15:18 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 = 3525 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: 2.400791 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): -38.47200 21.33000 ymin,ymax (A): -7.707000 46.39600 zmin,zma (A): -70.59200 -3.864000 x,y,z range (A): 59.80200 54.10300 66.72800 scale (grids/A): 2.400791 object centre (A): -8.571000 19.34450 -37.22800 number of atom coordinates read : 3525 total number of charged atoms : 3384 net assigned charge : -7.499971 assigned positive charge : 536.6349 centred at (gu) : 99.47024 95.04627 100.5158 assigned negative charge : -544.1368 centred at (gu) : 99.44815 94.92715 100.5821 start vw surface at 0.1800000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 166866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32049 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 76207 mr = 118722 m= 20699 mr = 59119 m= 3063 mr = 15105 m= 172 mr = 1873 m= 4 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 72151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 27031 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) : 1.600527 object centre at (A) : -8.571000 19.34450 -37.22800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5304018 -0.3859909 midg,1,midg; midg,igrid,midg -4.1585997E-02 -2.9457049E-02 1,midg,midg; igrid,midg,midg 6.1009335E-04 2.4833040E-02 gauss-seidel spectral radius is 0.9991403 estimated iterations to convergence 269 setup time was (sec) 1.540000 now iterating at: 03:15:20 rms-change max change #iterations 9.352765 303.5909 at 10iterations 5.292802 135.3363 at 20iterations 2.975701 82.46776 at 30iterations 1.660209 42.16117 at 40iterations 0.9240839 24.42030 at 50iterations 0.5135171 14.03869 at 60iterations 0.2845121 6.191962 at 70iterations 0.1573631 3.555892 at 80iterations 8.7191522E-02 1.996101 at 90iterations 4.8176087E-02 1.120501 at 100iterations 2.6587052E-02 0.5754204 at 110iterations 1.4678281E-02 0.3352394 at 120iterations 8.1083132E-03 0.1838584 at 130iterations 4.4921213E-03 9.5551014E-02 at 140iterations 2.4939808E-03 5.2823067E-02 at 150iterations 1.3963884E-03 2.9830933E-02 at 160iterations 7.9265318E-04 1.7768860E-02 at 170iterations 4.5881505E-04 1.0385990E-02 at 180iterations finished qdiffx linear iterations at : 03:15:30 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 4.5881505E-04 1.0385990E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 03:15:31 11.973u 0.245s 0:12.51 97.6% 0+0k 0+0io 0pf+0w