Tue Oct 11 04:53:45 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 04:53:45 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 = 2857 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: 0.6324391 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): -72.13700 -15.84700 ymin,ymax (A): -49.54800 2.728000 zmin,zma (A): 4.330000 60.58600 x,y,z range (A): 56.29000 52.27600 56.25600 scale (grids/A): 0.6324391 object centre (A): -43.99200 -23.41000 32.45800 number of atom coordinates read : 2857 total number of charged atoms : 2710 net assigned charge : 8.000020 assigned positive charge : 435.2705 centred at (gu) : 90.42949 90.03703 90.97391 assigned negative charge : -427.2713 centred at (gu) : 90.39575 89.76279 90.88035 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7693 nv = 96 ne = 84 npr = 56188 no. pairs analyzed = 56188 no. exposed pairs = 3645 no. arc points = 25547 no. surface atoms = 1229 nbur = 1628 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 431 mr = 4149 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3600000 number of dielectric boundary points 3940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2636 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9294 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9383127E-10 2.3333662E-08 midg,1,midg; midg,igrid,midg -2.0038231E-08 3.7287577E-08 1,midg,midg; igrid,midg,midg 5.2535034E-09 1.3977878E-08 gauss-seidel spectral radius is 0.9870753 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 04:53:46 rms-change max change #iterations 0.1409252 22.79894 at 10iterations 1.3985956E-02 1.869442 at 20iterations 1.3468027E-03 0.1781540 at 30iterations 1.3116287E-04 1.7573357E-02 at 40iterations 1.2599266E-05 1.6708374E-03 at 50iterations finished qdiffx linear iterations at : 04:53:49 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.2599266E-05 1.6708374E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 04:53:49 3.414u 0.145s 0:03.91 90.7% 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 04:53:49 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 = 2857 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.897317 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): -72.13700 -15.84700 ymin,ymax (A): -49.54800 2.728000 zmin,zma (A): 4.330000 60.58600 x,y,z range (A): 56.29000 52.27600 56.25600 scale (grids/A): 1.897317 object centre (A): -43.99200 -23.41000 32.45800 number of atom coordinates read : 2857 total number of charged atoms : 2710 net assigned charge : 8.000020 assigned positive charge : 435.2705 centred at (gu) : 91.28757 90.11052 92.92101 assigned negative charge : -427.2713 centred at (gu) : 91.18680 89.28820 92.64066 start vw surface at 0.2500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 82034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25547 grid for indexing accessible points = 1.400000 m= 30443 mr = 55957 m= 5052 mr = 22277 m= 290 mr = 3167 m= 3 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 654 time to turn everything in is 0.7600000 number of dielectric boundary points 36335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21284 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) : 0.6324391 object centre at (A) : -43.99200 -23.41000 32.45800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5667882E-02 4.2510439E-02 midg,1,midg; midg,igrid,midg -3.0218858E-02 5.4379143E-02 1,midg,midg; igrid,midg,midg 1.3389293E-03 5.4516707E-04 gauss-seidel spectral radius is 0.9986610 estimated iterations to convergence 217 setup time was (sec) 1.040000 now iterating at: 04:53:50 rms-change max change #iterations 4.473145 182.4853 at 10iterations 2.099101 71.87990 at 20iterations 0.9911300 34.60973 at 30iterations 0.4673953 14.44992 at 40iterations 0.2206105 6.470994 at 50iterations 0.1042367 3.201677 at 60iterations 4.8921470E-02 1.499491 at 70iterations 2.3142932E-02 0.7361487 at 80iterations 1.0915746E-02 0.3293831 at 90iterations 5.1443363E-03 0.1668491 at 100iterations 2.4312837E-03 7.7167511E-02 at 110iterations 1.1452599E-03 4.0269852E-02 at 120iterations finished qdiffx linear iterations at : 04:53:57 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.1452599E-03 4.0269852E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 04:53:58 7.802u 0.180s 0:08.78 90.8% 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 04:53:58 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 = 2857 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.845976 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): -72.13700 -15.84700 ymin,ymax (A): -49.54800 2.728000 zmin,zma (A): 4.330000 60.58600 x,y,z range (A): 56.29000 52.27600 56.25600 scale (grids/A): 2.845976 object centre (A): -43.99200 -23.41000 32.45800 number of atom coordinates read : 2857 total number of charged atoms : 2710 net assigned charge : 8.000020 assigned positive charge : 435.2705 centred at (gu) : 91.93146 90.16558 94.38155 assigned negative charge : -427.2713 centred at (gu) : 91.78008 88.93219 93.96077 start vw surface at 0.2300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 189361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25547 grid for indexing accessible points = 1.400000 m= 96815 mr = 135707 m= 36771 mr = 78710 m= 9139 mr = 29559 m= 1187 mr = 6746 m= 49 mr = 738 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 2343 time to turn everything in is 1.650000 number of dielectric boundary points 81850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 21676 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) : 1.897317 object centre at (A) : -43.99200 -23.41000 32.45800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4676921E-02 0.2610970 midg,1,midg; midg,igrid,midg -0.3185618 0.4082621 1,midg,midg; igrid,midg,midg -0.1415738 7.5926654E-02 gauss-seidel spectral radius is 0.9992706 estimated iterations to convergence 292 setup time was (sec) 1.970000 now iterating at: 04:54:00 rms-change max change #iterations 10.41383 415.0005 at 10iterations 6.098471 174.2879 at 20iterations 3.561423 70.99559 at 30iterations 2.071796 42.36544 at 40iterations 1.205534 23.92734 at 50iterations 0.6999013 13.45035 at 60iterations 0.4057336 9.089809 at 70iterations 0.2346760 4.708565 at 80iterations 0.1355879 2.488152 at 90iterations 7.8334488E-02 1.375168 at 100iterations 4.5223840E-02 0.8095055 at 110iterations 2.6154822E-02 0.4433255 at 120iterations 1.5091623E-02 0.2717757 at 130iterations 8.7140435E-03 0.1483994 at 140iterations 5.0351797E-03 8.3347321E-02 at 150iterations 2.9099660E-03 4.8414230E-02 at 160iterations 1.6743115E-03 3.0105591E-02 at 170iterations 9.6873438E-04 1.6366959E-02 at 180iterations finished qdiffx linear iterations at : 04:54:11 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 9.6873438E-04 1.6366959E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 04:54:11 12.410u 0.205s 0:12.91 97.6% 0+0k 0+0io 0pf+0w