Sat Oct 8 14:45:33 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 14:45:33 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 0.6382330 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): -12.21600 43.56300 ymin,ymax (A): -22.92700 22.32900 zmin,zma (A): -6.598000 48.01000 x,y,z range (A): 55.77900 45.25600 54.60800 scale (grids/A): 0.6382330 object centre (A): 15.67350 -0.2989998 20.70600 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : -1.985993 assigned positive charge : 454.5695 centred at (gu) : 88.86941 89.83413 91.14850 assigned negative charge : -456.5562 centred at (gu) : 88.82698 89.73464 91.11253 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8270 nv = 96 ne = 84 npr = 63350 no. pairs analyzed = 63350 no. exposed pairs = 3467 no. arc points = 24487 no. surface atoms = 1175 nbur = 1854 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 4851 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2346 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9952 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8003780E-09 2.5905438E-09 midg,1,midg; midg,igrid,midg -1.6396234E-08 9.7710897E-09 1,midg,midg; igrid,midg,midg -1.0547522E-08 2.1692634E-09 gauss-seidel spectral radius is 0.9873149 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 14:45:34 rms-change max change #iterations 0.1554057 21.81760 at 10iterations 1.5471303E-02 2.107201 at 20iterations 1.6010095E-03 0.2089221 at 30iterations 1.6821930E-04 2.0732880E-02 at 40iterations 2.0880509E-05 2.9029846E-03 at 50iterations finished qdiffx linear iterations at : 14:45:38 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 2.0880509E-05 2.9029846E-03 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 14:45:38 4.592u 0.395s 0:05.25 94.8% 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 Sat Oct 8 2011 at 14:45:38 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 1.914699 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): -12.21600 43.56300 ymin,ymax (A): -22.92700 22.32900 zmin,zma (A): -6.598000 48.01000 x,y,z range (A): 55.77900 45.25600 54.60800 scale (grids/A): 1.914699 object centre (A): 15.67350 -0.2989998 20.70600 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : -1.985993 assigned positive charge : 454.5695 centred at (gu) : 86.60773 89.50172 93.44483 assigned negative charge : -456.5562 centred at (gu) : 86.48051 89.20352 93.33730 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24487 grid for indexing accessible points = 1.400000 m= 32290 mr = 64893 m= 4706 mr = 24292 m= 274 mr = 2796 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 215 time to turn everything in is 0.7000000 number of dielectric boundary points 35117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22727 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) : 0.6382330 object centre at (A) : 15.67350 -0.2989998 20.70600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2494228E-02 3.1591502E-03 midg,1,midg; midg,igrid,midg -9.1088833E-03 1.6695362E-02 1,midg,midg; igrid,midg,midg -3.8515456E-02 1.5596260E-02 gauss-seidel spectral radius is 0.9986858 estimated iterations to convergence 219 setup time was (sec) 1.010000 now iterating at: 14:45:40 rms-change max change #iterations 4.707351 179.9038 at 10iterations 2.248585 64.27657 at 20iterations 1.068828 32.70515 at 30iterations 0.5086142 15.17689 at 40iterations 0.2418051 7.029190 at 50iterations 0.1153243 3.550013 at 60iterations 5.4804400E-02 1.608696 at 70iterations 2.6044209E-02 0.7378616 at 80iterations 1.2434896E-02 0.3666086 at 90iterations 5.9045698E-03 0.1773033 at 100iterations 2.8145129E-03 9.0805054E-02 at 110iterations 1.3452339E-03 3.8961411E-02 at 120iterations finished qdiffx linear iterations at : 14:45:49 total time elapsed so far: 10.68000 # loops : 120 mean,max change (kT/e) : 1.3452339E-03 3.8961411E-02 energy calculations done at 10.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.85000 DelPhi exited at 14:45:50 10.856u 0.442s 0:11.57 97.5% 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 Sat Oct 8 2011 at 14:45:50 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 2.872049 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): -12.21600 43.56300 ymin,ymax (A): -22.92700 22.32900 zmin,zma (A): -6.598000 48.01000 x,y,z range (A): 55.77900 45.25600 54.60800 scale (grids/A): 2.872049 object centre (A): 15.67350 -0.2989998 20.70600 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : -1.985993 assigned positive charge : 454.5695 centred at (gu) : 84.91149 89.25243 95.16698 assigned negative charge : -456.5562 centred at (gu) : 84.72072 88.80531 95.00598 start vw surface at 0.1300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 207890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24487 grid for indexing accessible points = 1.400000 m= 106635 mr = 156637 m= 37151 mr = 88957 m= 8289 mr = 29776 m= 1133 mr = 5988 m= 61 mr = 725 m= 0 mr = 39 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 737 time to turn everything in is 1.880000 number of dielectric boundary points 79037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 23056 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) : 1.914699 object centre at (A) : 15.67350 -0.2989998 20.70600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6765411E-02 0.1636200 midg,1,midg; midg,igrid,midg -7.9632580E-02 0.1886885 1,midg,midg; igrid,midg,midg -0.5759068 0.2272030 gauss-seidel spectral radius is 0.9992764 estimated iterations to convergence 293 setup time was (sec) 2.220000 now iterating at: 14:45:53 rms-change max change #iterations 11.00215 426.0817 at 10iterations 6.460372 125.1164 at 20iterations 3.772787 75.68433 at 30iterations 2.199366 37.30986 at 40iterations 1.279467 22.20401 at 50iterations 0.7426624 14.99340 at 60iterations 0.4318152 6.893223 at 70iterations 0.2503456 4.348598 at 80iterations 0.1451499 2.488774 at 90iterations 8.4117636E-02 1.583458 at 100iterations 4.8595965E-02 0.8852081 at 110iterations 2.8160131E-02 0.4793108 at 120iterations 1.6290115E-02 0.2552829 at 130iterations 9.4268098E-03 0.1543579 at 140iterations 5.4457327E-03 8.6265564E-02 at 150iterations 3.1525895E-03 5.4729462E-02 at 160iterations 1.8269427E-03 3.5479546E-02 at 170iterations 1.0573929E-03 1.6555786E-02 at 180iterations finished qdiffx linear iterations at : 14:46:09 total time elapsed so far: 18.26000 # loops : 180 mean,max change (kT/e) : 1.0573929E-03 1.6555786E-02 energy calculations done at 18.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.42000 DelPhi exited at 14:46:09 18.421u 0.463s 0:19.19 98.3% 0+0k 0+0io 0pf+0w