Sat Oct 8 11:36:36 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 Sat Oct 8 2011 at 11:36:37 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5134 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 470 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5414943 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): 7.306000 73.05000 ymin,ymax (A): 4.373000 65.95300 zmin,zma (A): 9.516000 75.23800 x,y,z range (A): 65.74400 61.58000 65.72200 scale (grids/A): 0.5414943 object centre (A): 40.17800 35.16300 42.37700 number of atom coordinates read : 5134 total number of charged atoms : 4962 net assigned charge : -5.1952899E-02 assigned positive charge : 781.1542 centred at (gu) : 90.36401 90.51199 90.81215 assigned negative charge : -781.2113 centred at (gu) : 90.28273 90.52027 90.86996 start vw surface at 0.2700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 9286 nv = 96 ne = 84 npr = 107771 no. pairs analyzed = 107771 no. exposed pairs = 5970 no. arc points = 40746 no. surface atoms = 2007 nbur = 3127 mkacc time = 0.3100000 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= 360 mr = 5101 m= 0 mr = 9 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.6400000 number of dielectric boundary points 4536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4178 ## 528 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 12543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6074528E-10 -7.0616779E-10 midg,1,midg; midg,igrid,midg 7.1551785E-11 -9.3049540E-11 1,midg,midg; igrid,midg,midg -7.3811063E-10 8.6967034E-10 gauss-seidel spectral radius is 0.9825663 estimated iterations to convergence 62 setup time was (sec) 0.9200000 now iterating at: 11:36:38 rms-change max change #iterations 9.6231073E-02 16.74269 at 10iterations 8.0426140E-03 1.373833 at 20iterations 1.4666376E-03 0.3448257 at 30iterations 3.9647048E-04 9.0728760E-02 at 40iterations 1.1176165E-04 2.4787903E-02 at 50iterations finished qdiffx linear iterations at : 11:36:41 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 1.1176165E-04 2.4787903E-02 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 11:36:41 4.379u 0.174s 0:04.94 91.9% 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 Sat Oct 8 2011 at 11:36:42 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5134 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 470 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.624483 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): 7.306000 73.05000 ymin,ymax (A): 4.373000 65.95300 zmin,zma (A): 9.516000 75.23800 x,y,z range (A): 65.74400 61.58000 65.72200 scale (grids/A): 1.624483 object centre (A): 40.17800 35.16300 42.37700 number of atom coordinates read : 5134 total number of charged atoms : 4962 net assigned charge : -5.1952899E-02 assigned positive charge : 781.1542 centred at (gu) : 91.09052 91.53419 92.43497 assigned negative charge : -781.2113 centred at (gu) : 90.84759 91.56059 92.60960 start vw surface at 0.2700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 104505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40746 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 32273 mr = 74075 m= 3288 mr = 22424 m= 75 mr = 1532 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 752 time to turn everything in is 0.9200000 number of dielectric boundary points 42105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 482 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 37952 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) : 0.5414943 object centre at (A) : 40.17800 35.16300 42.37700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3081658E-02 -8.1365202E-03 midg,1,midg; midg,igrid,midg -7.4320813E-03 -4.9028167E-04 1,midg,midg; igrid,midg,midg -8.9432029E-03 7.3324237E-03 gauss-seidel spectral radius is 0.9983660 estimated iterations to convergence 196 setup time was (sec) 1.260000 now iterating at: 11:36:43 rms-change max change #iterations 4.536936 184.9152 at 10iterations 1.976900 62.04358 at 20iterations 0.8628264 25.74552 at 30iterations 0.3777249 10.86953 at 40iterations 0.1652964 4.827037 at 50iterations 7.2210789E-02 1.959457 at 60iterations 3.1905707E-02 0.8883085 at 70iterations 1.4124705E-02 0.3938243 at 80iterations 6.3390657E-03 0.1957550 at 90iterations 2.9235375E-03 9.5436096E-02 at 100iterations 1.4039378E-03 5.3611755E-02 at 110iterations 7.2228833E-04 2.6855469E-02 at 120iterations finished qdiffx linear iterations at : 11:36:51 total time elapsed so far: 9.140000 # loops : 120 mean,max change (kT/e) : 7.2228833E-04 2.6855469E-02 energy calculations done at 9.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 11:36:51 9.375u 0.187s 0:09.84 97.0% 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 Sat Oct 8 2011 at 11:36:51 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5134 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 470 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.436724 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): 7.306000 73.05000 ymin,ymax (A): 4.373000 65.95300 zmin,zma (A): 9.516000 75.23800 x,y,z range (A): 65.74400 61.58000 65.72200 scale (grids/A): 2.436724 object centre (A): 40.17800 35.16300 42.37700 number of atom coordinates read : 5134 total number of charged atoms : 4962 net assigned charge : -5.1952899E-02 assigned positive charge : 781.1542 centred at (gu) : 91.63551 92.30094 93.65211 assigned negative charge : -781.2113 centred at (gu) : 91.27134 92.34074 93.91425 start vw surface at 0.2600000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 243539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40746 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 112323 mr = 181553 m= 32232 mr = 89263 m= 5022 mr = 24217 m= 326 mr = 3256 m= 3 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 1.350000 no. cavity mid-points inaccessible to solvent = 2614 time to turn everything in is 2.270000 number of dielectric boundary points 95022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.440000 number of grid points assigned charge 39643 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) : 1.624483 object centre at (A) : 40.17800 35.16300 42.37700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3366164 -0.2855332 midg,1,midg; midg,igrid,midg -0.1512109 -6.7034595E-02 1,midg,midg; igrid,midg,midg -0.1895277 -4.5486189E-02 gauss-seidel spectral radius is 0.9992405 estimated iterations to convergence 286 setup time was (sec) 2.640000 now iterating at: 11:36:54 rms-change max change #iterations 11.88999 295.6902 at 10iterations 7.035550 167.0117 at 20iterations 4.148242 78.35162 at 30iterations 2.425214 45.95950 at 40iterations 1.414168 26.32394 at 50iterations 0.8238578 16.43630 at 60iterations 0.4771868 9.739404 at 70iterations 0.2764101 5.383029 at 80iterations 0.1596895 2.933683 at 90iterations 9.2218176E-02 1.675644 at 100iterations 5.3409565E-02 1.049692 at 110iterations 3.0799164E-02 0.6039581 at 120iterations 1.7767215E-02 0.3018751 at 130iterations 1.0282854E-02 0.2134085 at 140iterations 5.9659411E-03 0.1078091 at 150iterations 3.4754432E-03 6.1592102E-02 at 160iterations 2.0475611E-03 3.6476135E-02 at 170iterations 1.2208844E-03 2.3162842E-02 at 180iterations finished qdiffx linear iterations at : 11:37:07 total time elapsed so far: 15.24000 # loops : 180 mean,max change (kT/e) : 1.2208844E-03 2.3162842E-02 energy calculations done at 15.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.48000 DelPhi exited at 11:37:07 15.479u 0.195s 0:15.94 98.2% 0+0k 0+0io 0pf+0w