Tue Oct 11 04:53:03 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 Tue Oct 11 2011 at 04:53:03 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7225345 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): 1.591000 45.94400 ymin,ymax (A): 0.5260001 41.45800 zmin,zma (A): -2.220000 47.05100 x,y,z range (A): 44.35300 40.93200 49.27100 scale (grids/A): 0.7225345 object centre (A): 23.76750 20.99200 22.41550 number of atom coordinates read : 2089 total number of charged atoms : 1959 net assigned charge : 6.039011 assigned positive charge : 323.1360 centred at (gu) : 91.07949 90.21890 90.49312 assigned negative charge : -317.0970 centred at (gu) : 91.21845 90.20188 90.57008 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7348 nv = 96 ne = 84 npr = 42617 no. pairs analyzed = 42617 no. exposed pairs = 2480 no. arc points = 16862 no. surface atoms = 848 nbur = 1241 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 536 mr = 4291 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1589 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8085 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1574787E-07 2.1150246E-08 midg,1,midg; midg,igrid,midg 5.9421652E-08 8.9155066E-08 1,midg,midg; igrid,midg,midg 1.3803916E-07 -3.1589234E-08 gauss-seidel spectral radius is 0.9900090 estimated iterations to convergence 81 setup time was (sec) 0.5300000 now iterating at: 04:53:04 rms-change max change #iterations 0.2250661 34.77001 at 10iterations 2.9842386E-02 3.909012 at 20iterations 4.0977537E-03 0.4705143 at 30iterations 7.2177139E-04 8.9030266E-02 at 40iterations 1.9075154E-04 2.6475906E-02 at 50iterations finished qdiffx linear iterations at : 04:53:07 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.9075154E-04 2.6475906E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 04:53:07 3.378u 0.195s 0:03.89 91.5% 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 Tue Oct 11 2011 at 04:53:07 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.167603 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): 1.591000 45.94400 ymin,ymax (A): 0.5260001 41.45800 zmin,zma (A): -2.220000 47.05100 x,y,z range (A): 44.35300 40.93200 49.27100 scale (grids/A): 2.167603 object centre (A): 23.76750 20.99200 22.41550 number of atom coordinates read : 2089 total number of charged atoms : 1959 net assigned charge : 6.039011 assigned positive charge : 323.1360 centred at (gu) : 93.23850 90.65675 91.47952 assigned negative charge : -317.0970 centred at (gu) : 93.65522 90.60562 91.71027 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 32042 mr = 56039 m= 6397 mr = 24463 m= 530 mr = 4205 m= 7 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 32038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15560 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) : 0.7225345 object centre at (A) : 23.76750 20.99200 22.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5758303E-02 8.3413593E-02 midg,1,midg; midg,igrid,midg 2.7309461E-03 3.0278303E-02 1,midg,midg; igrid,midg,midg 3.0926123E-02 1.7263630E-02 gauss-seidel spectral radius is 0.9988704 estimated iterations to convergence 235 setup time was (sec) 0.8800000 now iterating at: 04:53:08 rms-change max change #iterations 4.871181 197.2567 at 10iterations 2.439873 85.54228 at 20iterations 1.230968 34.24510 at 30iterations 0.6176363 18.40806 at 40iterations 0.3119261 8.890579 at 50iterations 0.1568458 4.339447 at 60iterations 7.9015598E-02 2.203608 at 70iterations 3.9628766E-02 1.215652 at 80iterations 1.9956505E-02 0.6138802 at 90iterations 1.0166653E-02 0.2813187 at 100iterations 5.1387809E-03 0.1478462 at 110iterations 2.6467864E-03 7.1853638E-02 at 120iterations finished qdiffx linear iterations at : 04:53:15 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 2.6467864E-03 7.1853638E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 04:53:15 7.725u 0.241s 0:08.30 95.9% 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 Tue Oct 11 2011 at 04:53:16 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.251405 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): 1.591000 45.94400 ymin,ymax (A): 0.5260001 41.45800 zmin,zma (A): -2.220000 47.05100 x,y,z range (A): 44.35300 40.93200 49.27100 scale (grids/A): 3.251405 object centre (A): 23.76750 20.99200 22.41550 number of atom coordinates read : 2089 total number of charged atoms : 1959 net assigned charge : 6.039011 assigned positive charge : 323.1360 centred at (gu) : 94.85786 90.98516 92.21918 assigned negative charge : -317.0970 centred at (gu) : 95.48286 90.90846 92.56529 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 179586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 99322 mr = 134596 m= 41280 mr = 83015 m= 12137 mr = 34067 m= 2322 mr = 9377 m= 226 mr = 1567 m= 3 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 72122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 15672 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) : 2.167603 object centre at (A) : 23.76750 20.99200 22.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6410005 0.8791606 midg,1,midg; midg,igrid,midg -2.5674026E-02 0.2466848 1,midg,midg; igrid,midg,midg 0.2475319 0.4431264 gauss-seidel spectral radius is 0.9993042 estimated iterations to convergence 299 setup time was (sec) 2.170000 now iterating at: 04:53:18 rms-change max change #iterations 10.74263 328.8872 at 10iterations 6.388859 144.1783 at 20iterations 3.787288 79.20422 at 30iterations 2.242178 47.31348 at 40iterations 1.325446 28.53049 at 50iterations 0.7799677 15.89616 at 60iterations 0.4609385 8.181824 at 70iterations 0.2710561 4.525932 at 80iterations 0.1599368 2.826929 at 90iterations 9.4127655E-02 1.800140 at 100iterations 5.5653095E-02 1.000084 at 110iterations 3.3013847E-02 0.6308441 at 120iterations 1.9761885E-02 0.3498840 at 130iterations 1.2107549E-02 0.2177277 at 140iterations 7.6356693E-03 0.1280136 at 150iterations 5.0208736E-03 9.5451355E-02 at 160iterations 3.4942569E-03 6.4170837E-02 at 170iterations 2.5826523E-03 4.4761658E-02 at 180iterations finished qdiffx linear iterations at : 04:53:28 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 2.5826523E-03 4.4761658E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 04:53:29 12.765u 0.214s 0:13.34 97.2% 0+0k 0+0io 0pf+0w