Mon Oct 10 17:08:19 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+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 Mon Oct 10 2011 at 17:08:19 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5401140 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): -42.63500 7.057000 ymin,ymax (A): -67.16700 -1.255000 zmin,zma (A): -17.59800 29.49600 x,y,z range (A): 49.69200 65.91200 47.09400 scale (grids/A): 0.5401140 object centre (A): -17.78900 -34.21100 5.949000 number of atom coordinates read : 2701 total number of charged atoms : 2524 net assigned charge : 8.000022 assigned positive charge : 397.6557 centred at (gu) : 89.64129 90.96159 90.65829 assigned negative charge : -389.6567 centred at (gu) : 89.76595 90.87517 90.70022 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5194 nv = 96 ne = 84 npr = 53710 no. pairs analyzed = 53710 no. exposed pairs = 3611 no. arc points = 25413 no. surface atoms = 1212 nbur = 1489 mkacc time = 8.9999996E-02 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 = 1.596000 m= 198 mr = 2556 m= 0 mr = 7 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2634 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6729 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9710769E-10 2.2509483E-10 midg,1,midg; midg,igrid,midg -1.0265295E-11 1.0025301E-09 1,midg,midg; igrid,midg,midg 1.0522370E-09 -1.8170439E-10 gauss-seidel spectral radius is 0.9823141 estimated iterations to convergence 62 setup time was (sec) 0.3800000 now iterating at: 17:08:20 rms-change max change #iterations 6.2026449E-02 10.45041 at 10iterations 3.9942665E-03 0.6016846 at 20iterations 3.0005642E-04 5.5613518E-02 at 30iterations 3.4889057E-05 6.7119598E-03 at 40iterations 6.1583660E-06 1.3818741E-03 at 50iterations finished qdiffx linear iterations at : 17:08:22 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 6.1583660E-06 1.3818741E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 17:08:23 3.361u 0.166s 0:03.89 90.4% 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 Mon Oct 10 2011 at 17:08:23 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.620342 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): -42.63500 7.057000 ymin,ymax (A): -67.16700 -1.255000 zmin,zma (A): -17.59800 29.49600 x,y,z range (A): 49.69200 65.91200 47.09400 scale (grids/A): 1.620342 object centre (A): -17.78900 -34.21100 5.949000 number of atom coordinates read : 2701 total number of charged atoms : 2524 net assigned charge : 8.000022 assigned positive charge : 397.6557 centred at (gu) : 88.92323 92.88412 91.97420 assigned negative charge : -389.6567 centred at (gu) : 89.29753 92.62537 92.10038 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 56834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25413 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17727 mr = 37408 m= 1925 mr = 11912 m= 43 mr = 891 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.2800000 number of dielectric boundary points 26318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 19259 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) : 0.5401140 object centre at (A) : -17.78900 -34.21100 5.949000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8195023E-03 -3.1321732E-05 midg,1,midg; midg,igrid,midg 8.6799841E-03 2.3604056E-02 1,midg,midg; igrid,midg,midg 1.1169162E-02 -6.8902136E-03 gauss-seidel spectral radius is 0.9981284 estimated iterations to convergence 184 setup time was (sec) 0.4900000 now iterating at: 17:08:24 rms-change max change #iterations 3.012828 135.4415 at 10iterations 1.238404 48.92828 at 20iterations 0.5103047 20.68747 at 30iterations 0.2092158 7.909195 at 40iterations 8.6269312E-02 3.975010 at 50iterations 3.5424411E-02 1.326551 at 60iterations 1.4510317E-02 0.5993671 at 70iterations 5.9978920E-03 0.2241642 at 80iterations 2.4669396E-03 9.5880032E-02 at 90iterations 1.0203230E-03 4.1342735E-02 at 100iterations 4.2277307E-04 1.6674042E-02 at 110iterations 1.7656511E-04 8.3332062E-03 at 120iterations finished qdiffx linear iterations at : 17:08:31 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 1.7656511E-04 8.3332062E-03 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 17:08:31 7.537u 0.202s 0:08.04 96.1% 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 Mon Oct 10 2011 at 17:08:31 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.430513 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): -42.63500 7.057000 ymin,ymax (A): -67.16700 -1.255000 zmin,zma (A): -17.59800 29.49600 x,y,z range (A): 49.69200 65.91200 47.09400 scale (grids/A): 2.430513 object centre (A): -17.78900 -34.21100 5.949000 number of atom coordinates read : 2701 total number of charged atoms : 2524 net assigned charge : 8.000022 assigned positive charge : 397.6557 centred at (gu) : 88.38453 94.32594 92.96123 assigned negative charge : -389.6567 centred at (gu) : 88.94632 93.93794 93.15045 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 131937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25413 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 60531 mr = 91714 m= 17516 mr = 47156 m= 2902 mr = 12909 m= 189 mr = 1850 m= 5 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 470 time to turn everything in is 0.7000000 number of dielectric boundary points 59394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20161 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) : 1.620342 object centre at (A) : -17.78900 -34.21100 5.949000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1799293E-02 -8.0531593E-03 midg,1,midg; midg,igrid,midg 0.1991287 0.3734426 1,midg,midg; igrid,midg,midg 0.1678673 -7.9698369E-02 gauss-seidel spectral radius is 0.9991173 estimated iterations to convergence 266 setup time was (sec) 0.9200000 now iterating at: 17:08:32 rms-change max change #iterations 7.963522 286.8121 at 10iterations 4.447917 143.1412 at 20iterations 2.471497 73.88199 at 30iterations 1.359647 33.76601 at 40iterations 0.7490298 18.05230 at 50iterations 0.4111438 10.69971 at 60iterations 0.2252852 5.446433 at 70iterations 0.1230804 2.936478 at 80iterations 6.7197636E-02 1.571449 at 90iterations 3.6791947E-02 0.8869777 at 100iterations 2.0032682E-02 0.4565315 at 110iterations 1.0935053E-02 0.2452698 at 120iterations 5.9651863E-03 0.1247501 at 130iterations 3.2565068E-03 7.0205688E-02 at 140iterations 1.7743527E-03 4.2437553E-02 at 150iterations 9.6790673E-04 2.1757126E-02 at 160iterations 5.2991096E-04 1.1375427E-02 at 170iterations 2.9011784E-04 6.4420700E-03 at 180iterations finished qdiffx linear iterations at : 17:08:43 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 2.9011784E-04 6.4420700E-03 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 17:08:44 11.949u 0.194s 0:12.63 96.0% 0+0k 0+0io 0pf+0w