Mon Oct 10 17:03:23 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 17:03:23 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5228 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5062283 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): -18.87100 37.01800 ymin,ymax (A): -30.76500 32.36600 zmin,zma (A): -3.940000 66.38400 x,y,z range (A): 55.88900 63.13100 70.32400 scale (grids/A): 0.5062283 object centre (A): 9.073501 0.8004999 31.22200 number of atom coordinates read : 5228 total number of charged atoms : 4976 net assigned charge : 5.800026 assigned positive charge : 786.6003 centred at (gu) : 90.51068 90.76244 89.41016 assigned negative charge : -780.8057 centred at (gu) : 90.43449 90.78490 89.40178 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8400 nv = 96 ne = 84 npr = 106661 no. pairs analyzed = 106661 no. exposed pairs = 6422 no. arc points = 44516 no. surface atoms = 2181 nbur = 3047 mkacc time = 0.3000000 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 = 1.680000 m= 305 mr = 4423 m= 0 mr = 11 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 4271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4318 ## 671 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 11235 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5104060E-11 7.4472886E-11 midg,1,midg; midg,igrid,midg 9.8020946E-11 1.6802251E-11 1,midg,midg; igrid,midg,midg -9.8627648E-11 2.7988828E-10 gauss-seidel spectral radius is 0.9800742 estimated iterations to convergence 59 setup time was (sec) 0.8600000 now iterating at: 17:03:24 rms-change max change #iterations 6.8556242E-02 10.03959 at 10iterations 4.1699726E-03 0.5805054 at 20iterations 5.8467692E-04 8.3511353E-02 at 30iterations 1.8318294E-04 2.0195007E-02 at 40iterations 6.5747598E-05 7.3194504E-03 at 50iterations finished qdiffx linear iterations at : 17:03:27 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 6.5747598E-05 7.3194504E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 17:03:29 4.331u 0.285s 0:05.81 79.3% 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 17:03:29 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5228 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.518685 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): -18.87100 37.01800 ymin,ymax (A): -30.76500 32.36600 zmin,zma (A): -3.940000 66.38400 x,y,z range (A): 55.88900 63.13100 70.32400 scale (grids/A): 1.518685 object centre (A): 9.073501 0.8004999 31.22200 number of atom coordinates read : 5228 total number of charged atoms : 4976 net assigned charge : 5.800026 assigned positive charge : 786.6003 centred at (gu) : 91.53065 92.28580 88.22874 assigned negative charge : -780.8057 centred at (gu) : 91.30330 92.35418 88.20509 start vw surface at 0.2300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 95722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44516 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27439 mr = 66613 m= 2422 mr = 17945 m= 68 mr = 1003 m= 0 mr = 2 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 40088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 583 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 37262 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) : 0.5062283 object centre at (A) : 9.073501 0.8004999 31.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6502925E-03 1.4440679E-02 midg,1,midg; midg,igrid,midg -2.3184987E-04 -1.3885173E-02 1,midg,midg; igrid,midg,midg -1.5506801E-03 1.1011085E-02 gauss-seidel spectral radius is 0.9981134 estimated iterations to convergence 183 setup time was (sec) 1.150000 now iterating at: 17:03:30 rms-change max change #iterations 3.926899 158.4159 at 10iterations 1.611396 55.39018 at 20iterations 0.6613335 23.01850 at 30iterations 0.2721425 8.532705 at 40iterations 0.1114374 3.489418 at 50iterations 4.5662291E-02 1.528872 at 60iterations 1.8862654E-02 0.5514450 at 70iterations 7.7689253E-03 0.2417688 at 80iterations 3.2180268E-03 9.6485138E-02 at 90iterations 1.3542584E-03 4.3373108E-02 at 100iterations 5.9201347E-04 1.7589569E-02 at 110iterations 2.8140438E-04 8.5754395E-03 at 120iterations finished qdiffx linear iterations at : 17:03:39 total time elapsed so far: 9.600000 # loops : 120 mean,max change (kT/e) : 2.8140438E-04 8.5754395E-03 energy calculations done at 9.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.780000 DelPhi exited at 17:03:41 9.782u 0.307s 0:12.00 84.0% 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 Mon Oct 10 2011 at 17:03:41 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5228 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.278028 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): -18.87100 37.01800 ymin,ymax (A): -30.76500 32.36600 zmin,zma (A): -3.940000 66.38400 x,y,z range (A): 55.88900 63.13100 70.32400 scale (grids/A): 2.278028 object centre (A): 9.073501 0.8004999 31.22200 number of atom coordinates read : 5228 total number of charged atoms : 4976 net assigned charge : 5.800026 assigned positive charge : 786.6003 centred at (gu) : 92.29555 93.42853 87.34277 assigned negative charge : -780.8057 centred at (gu) : 91.95486 93.53136 87.30758 start vw surface at 0.2400000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 223599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44516 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 98980 mr = 163613 m= 24435 mr = 77206 m= 3447 mr = 17228 m= 196 mr = 1990 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 90557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 39682 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) : 1.518685 object centre at (A) : 9.073501 0.8004999 31.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1634266 0.2737591 midg,1,midg; midg,igrid,midg -7.5515166E-02 -0.3426720 1,midg,midg; igrid,midg,midg -2.3478447E-02 0.1651312 gauss-seidel spectral radius is 0.9991721 estimated iterations to convergence 274 setup time was (sec) 2.450000 now iterating at: 17:03:44 rms-change max change #iterations 10.71524 258.4005 at 10iterations 6.159018 152.6528 at 20iterations 3.521901 73.98302 at 30iterations 2.001158 40.23617 at 40iterations 1.131983 24.19703 at 50iterations 0.6376393 13.46293 at 60iterations 0.3586930 6.737334 at 70iterations 0.2012333 4.070847 at 80iterations 0.1126456 2.110569 at 90iterations 6.3094325E-02 1.145338 at 100iterations 3.5304159E-02 0.7368317 at 110iterations 1.9675529E-02 0.3629303 at 120iterations 1.1011311E-02 0.2031670 at 130iterations 6.1478699E-03 0.1136322 at 140iterations 3.4317784E-03 5.9993744E-02 at 150iterations 1.9165232E-03 3.4014702E-02 at 160iterations 1.0752238E-03 2.0217896E-02 at 170iterations 6.0384942E-04 1.1784554E-02 at 180iterations finished qdiffx linear iterations at : 17:03:58 total time elapsed so far: 16.62000 # loops : 180 mean,max change (kT/e) : 6.0384942E-04 1.1784554E-02 energy calculations done at 16.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.80000 DelPhi exited at 17:04:00 16.797u 0.298s 0:18.79 90.8% 0+0k 0+0io 0pf+0w