Tue Oct 11 06:02:17 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 06:02:18 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 0.7066997 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): 25.66500 72.09299 ymin,ymax (A): -18.77500 31.60000 zmin,zma (A): 3.885000 46.29800 x,y,z range (A): 46.42799 50.37500 42.41300 scale (grids/A): 0.7066997 object centre (A): 48.87900 6.412500 25.09150 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 89.19916 90.19070 90.36620 assigned negative charge : -317.2741 centred at (gu) : 89.32887 90.13828 90.44934 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7196 nv = 96 ne = 84 npr = 42497 no. pairs analyzed = 42497 no. exposed pairs = 2581 no. arc points = 17478 no. surface atoms = 887 nbur = 1431 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 463 mr = 4180 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1605 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7978 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7822343E-08 1.2674496E-08 midg,1,midg; midg,igrid,midg 2.6507298E-08 8.2211585E-08 1,midg,midg; igrid,midg,midg 1.3657281E-07 -9.3758263E-09 gauss-seidel spectral radius is 0.9895653 estimated iterations to convergence 80 setup time was (sec) 0.3700000 now iterating at: 06:02:18 rms-change max change #iterations 0.2009617 29.46055 at 10iterations 2.5100036E-02 3.779678 at 20iterations 3.2244690E-03 0.4082184 at 30iterations 5.0601189E-04 7.4485779E-02 at 40iterations 1.1864824E-04 1.4883041E-02 at 50iterations finished qdiffx linear iterations at : 06:02:21 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.1864824E-04 1.4883041E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 06:02:22 3.408u 0.183s 0:04.22 84.8% 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 06:02:22 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 2.120099 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): 25.66500 72.09299 ymin,ymax (A): -18.77500 31.60000 zmin,zma (A): 3.885000 46.29800 x,y,z range (A): 46.42799 50.37500 42.41300 scale (grids/A): 2.120099 object centre (A): 48.87900 6.412500 25.09150 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 87.59750 90.57197 91.09855 assigned negative charge : -317.2741 centred at (gu) : 87.98666 90.41497 91.34806 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17478 grid for indexing accessible points = 1.400000 m= 31182 mr = 54517 m= 5960 mr = 23878 m= 546 mr = 4020 m= 15 mr = 293 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 31294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15832 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) : 0.7066997 object centre at (A) : 48.87900 6.412500 25.09150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0788653E-02 2.9629648E-02 midg,1,midg; midg,igrid,midg 4.6449758E-02 2.7694715E-02 1,midg,midg; igrid,midg,midg 4.4922281E-02 -5.0474107E-02 gauss-seidel spectral radius is 0.9988314 estimated iterations to convergence 232 setup time was (sec) 0.6200000 now iterating at: 06:02:23 rms-change max change #iterations 4.639647 189.7509 at 10iterations 2.292747 81.84810 at 20iterations 1.137458 34.07825 at 30iterations 0.5653777 17.43552 at 40iterations 0.2813725 8.324371 at 50iterations 0.1395356 4.090576 at 60iterations 6.9226474E-02 2.172677 at 70iterations 3.4465365E-02 0.9669409 at 80iterations 1.7204879E-02 0.5454473 at 90iterations 8.6007211E-03 0.2779617 at 100iterations 4.3281158E-03 0.1407166 at 110iterations 2.2158576E-03 6.6686630E-02 at 120iterations finished qdiffx linear iterations at : 06:02:30 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.2158576E-03 6.6686630E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 06:02:30 7.939u 0.208s 0:08.55 95.0% 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 Tue Oct 11 2011 at 06:02:31 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 3.180149 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): 25.66500 72.09299 ymin,ymax (A): -18.77500 31.60000 zmin,zma (A): 3.885000 46.29800 x,y,z range (A): 46.42799 50.37500 42.41300 scale (grids/A): 3.180149 object centre (A): 48.87900 6.412500 25.09150 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 86.39615 90.85793 91.64783 assigned negative charge : -317.2741 centred at (gu) : 86.98011 90.62247 92.02209 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 175615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17478 grid for indexing accessible points = 1.400000 m= 96751 mr = 131004 m= 39777 mr = 80956 m= 11340 mr = 32932 m= 2199 mr = 8806 m= 262 mr = 1601 m= 18 mr = 175 m= 0 mr = 9 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.210000 number of dielectric boundary points 70479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 15952 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) : 2.120099 object centre at (A) : 48.87900 6.412500 25.09150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1246882 0.2493055 midg,1,midg; midg,igrid,midg 0.3536622 0.1306731 1,midg,midg; igrid,midg,midg 0.4215984 -0.6115928 gauss-seidel spectral radius is 0.9992977 estimated iterations to convergence 298 setup time was (sec) 1.450000 now iterating at: 06:02:32 rms-change max change #iterations 10.29072 355.5479 at 10iterations 6.087981 150.6182 at 20iterations 3.606242 73.93694 at 30iterations 2.124510 43.00861 at 40iterations 1.251354 24.16589 at 50iterations 0.7366046 14.35406 at 60iterations 0.4330238 8.044168 at 70iterations 0.2539954 5.120337 at 80iterations 0.1489879 2.666253 at 90iterations 8.7340578E-02 1.545158 at 100iterations 5.1408265E-02 0.9151583 at 110iterations 3.0261453E-02 0.5387497 at 120iterations 1.7857516E-02 0.3033166 at 130iterations 1.0711911E-02 0.1854744 at 140iterations 6.5160110E-03 0.1207714 at 150iterations 4.0711323E-03 7.0350647E-02 at 160iterations 2.6605271E-03 5.4283142E-02 at 170iterations 1.8411470E-03 3.5217285E-02 at 180iterations finished qdiffx linear iterations at : 06:02:44 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.8411470E-03 3.5217285E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 06:02:44 12.996u 0.202s 0:13.68 96.4% 0+0k 0+0io 0pf+0w