Sun Oct 9 16:09:29 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 Sun Oct 9 2011 at 16:09:29 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3104 !!! WARNING: GLM 226 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6162794 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): -15.77500 36.29200 ymin,ymax (A): 55.29700 108.0610 zmin,zma (A): -5.285000 52.48100 x,y,z range (A): 52.06700 52.76401 57.76600 scale (grids/A): 0.6162794 object centre (A): 10.25850 81.67900 23.59800 number of atom coordinates read : 3104 total number of charged atoms : 2955 net assigned charge : -3.593989 assigned positive charge : 460.3291 centred at (gu) : 90.37804 88.90226 90.85779 assigned negative charge : -463.9244 centred at (gu) : 90.44659 88.74738 90.95809 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7555 nv = 96 ne = 84 npr = 65430 no. pairs analyzed = 65430 no. exposed pairs = 3815 no. arc points = 26526 no. surface atoms = 1285 nbur = 1819 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 4020 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2590 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9402 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8682400E-09 -1.1570642E-08 midg,1,midg; midg,igrid,midg -1.7342128E-08 6.6095729E-09 1,midg,midg; igrid,midg,midg 2.2852951E-09 -7.8820559E-09 gauss-seidel spectral radius is 0.9864048 estimated iterations to convergence 70 setup time was (sec) 0.4200000 now iterating at: 16:09:30 rms-change max change #iterations 0.1378633 23.10715 at 10iterations 1.2429258E-02 1.854774 at 20iterations 1.2458508E-03 0.2104301 at 30iterations 1.6771429E-04 3.6716461E-02 at 40iterations 3.4893263E-05 9.1972351E-03 at 50iterations finished qdiffx linear iterations at : 16:09:33 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 3.4893263E-05 9.1972351E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 16:09:33 3.426u 0.174s 0:03.94 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 Sun Oct 9 2011 at 16:09:33 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3104 !!! WARNING: GLM 226 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.848838 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): -15.77500 36.29200 ymin,ymax (A): 55.29700 108.0610 zmin,zma (A): -5.285000 52.48100 x,y,z range (A): 52.06700 52.76401 57.76600 scale (grids/A): 1.848838 object centre (A): 10.25850 81.67900 23.59800 number of atom coordinates read : 3104 total number of charged atoms : 2955 net assigned charge : -3.593989 assigned positive charge : 460.3291 centred at (gu) : 91.13358 86.70632 92.57274 assigned negative charge : -463.9244 centred at (gu) : 91.33944 86.24212 92.87415 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80835 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26526 grid for indexing accessible points = 1.400000 m= 29640 mr = 55247 m= 5177 mr = 21323 m= 258 mr = 3168 m= 5 mr = 70 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 36107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23146 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) : 0.6162794 object centre at (A) : 10.25850 81.67900 23.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1983266E-02 4.8765116E-03 midg,1,midg; midg,igrid,midg -3.8943794E-02 -5.1584528E-03 1,midg,midg; igrid,midg,midg 1.4524079E-03 -3.2324765E-02 gauss-seidel spectral radius is 0.9985951 estimated iterations to convergence 211 setup time was (sec) 0.6200000 now iterating at: 16:09:34 rms-change max change #iterations 4.440347 186.3995 at 10iterations 2.047812 73.67090 at 20iterations 0.9497883 30.98008 at 30iterations 0.4395365 13.47780 at 40iterations 0.2031012 6.917171 at 50iterations 9.4644561E-02 2.951454 at 60iterations 4.3666635E-02 1.248103 at 70iterations 2.0274408E-02 0.6238861 at 80iterations 9.4243921E-03 0.3139954 at 90iterations 4.3773870E-03 0.1343403 at 100iterations 2.0339733E-03 6.2668800E-02 at 110iterations 9.4952475E-04 2.9323578E-02 at 120iterations finished qdiffx linear iterations at : 16:09:41 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 9.4952475E-04 2.9323578E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 16:09:42 7.879u 0.198s 0:08.35 96.5% 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 Sun Oct 9 2011 at 16:09:42 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3104 !!! WARNING: GLM 226 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.773257 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): -15.77500 36.29200 ymin,ymax (A): 55.29700 108.0610 zmin,zma (A): -5.285000 52.48100 x,y,z range (A): 52.06700 52.76401 57.76600 scale (grids/A): 2.773257 object centre (A): 10.25850 81.67900 23.59800 number of atom coordinates read : 3104 total number of charged atoms : 2955 net assigned charge : -3.593989 assigned positive charge : 460.3291 centred at (gu) : 91.70012 85.05945 93.85878 assigned negative charge : -463.9244 centred at (gu) : 92.00906 84.36301 94.31128 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 186908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26526 grid for indexing accessible points = 1.400000 m= 93527 mr = 134421 m= 36035 mr = 75104 m= 9416 mr = 28572 m= 1250 mr = 6895 m= 50 mr = 740 m= 0 mr = 1 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 81453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 23636 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) : 1.848838 object centre at (A) : 10.25850 81.67900 23.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4750268 0.2201821 midg,1,midg; midg,igrid,midg -0.3594765 -0.1949937 1,midg,midg; igrid,midg,midg 2.7457669E-02 -0.3698688 gauss-seidel spectral radius is 0.9992602 estimated iterations to convergence 290 setup time was (sec) 1.310000 now iterating at: 16:09:43 rms-change max change #iterations 10.71976 340.1942 at 10iterations 6.316129 161.3075 at 20iterations 3.709273 89.83170 at 30iterations 2.163604 46.38560 at 40iterations 1.261572 29.18646 at 50iterations 0.7320328 15.52071 at 60iterations 0.4233328 8.193302 at 70iterations 0.2457780 5.149231 at 80iterations 0.1417931 2.719364 at 90iterations 8.1814028E-02 1.578094 at 100iterations 4.7223352E-02 0.8860283 at 110iterations 2.7220039E-02 0.5128622 at 120iterations 1.5700407E-02 0.3113091 at 130iterations 9.0507548E-03 0.1731987 at 140iterations 5.2128872E-03 0.1011333 at 150iterations 3.0027265E-03 5.6297302E-02 at 160iterations 1.7314083E-03 3.2087326E-02 at 170iterations 1.0042321E-03 1.7148972E-02 at 180iterations finished qdiffx linear iterations at : 16:09:55 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 1.0042321E-03 1.7148972E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 16:09:55 12.875u 0.206s 0:13.37 97.7% 0+0k 0+0io 0pf+0w