Mon Oct 10 19:32:07 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 Mon Oct 10 2011 at 19:32:07 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2418 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7116299 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): -14.63800 32.32800 ymin,ymax (A): -6.705000 40.30100 zmin,zma (A): 36.21900 86.24500 x,y,z range (A): 46.96600 47.00600 50.02600 scale (grids/A): 0.7116299 object centre (A): 8.844999 16.79800 61.23200 number of atom coordinates read : 2418 total number of charged atoms : 2281 net assigned charge : 1.014006 assigned positive charge : 363.7628 centred at (gu) : 89.09290 91.54294 88.68275 assigned negative charge : -362.7495 centred at (gu) : 89.24574 91.53734 88.64427 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8650 nv = 96 ne = 84 npr = 48290 no. pairs analyzed = 48290 no. exposed pairs = 3178 no. arc points = 21965 no. surface atoms = 1054 nbur = 1364 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 649 mr = 4810 m= 5 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3000000 number of dielectric boundary points 4355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1967 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9351 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0320398E-08 2.5462843E-08 midg,1,midg; midg,igrid,midg 4.0218024E-09 1.6538289E-08 1,midg,midg; igrid,midg,midg 1.2372098E-07 -7.4009399E-08 gauss-seidel spectral radius is 0.9897503 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 19:32:08 rms-change max change #iterations 0.2227738 35.12233 at 10iterations 2.8301565E-02 3.277115 at 20iterations 3.9894991E-03 0.5122337 at 30iterations 1.0145766E-03 0.1286087 at 40iterations 4.2192647E-04 5.1660538E-02 at 50iterations finished qdiffx linear iterations at : 19:32:11 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 4.2192647E-04 5.1660538E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 19:32:12 3.405u 0.255s 0:04.11 88.8% 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 Mon Oct 10 2011 at 19:32:12 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2418 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.134890 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): -14.63800 32.32800 ymin,ymax (A): -6.705000 40.30100 zmin,zma (A): 36.21900 86.24500 x,y,z range (A): 46.96600 47.00600 50.02600 scale (grids/A): 2.134890 object centre (A): 8.844999 16.79800 61.23200 number of atom coordinates read : 2418 total number of charged atoms : 2281 net assigned charge : 1.014006 assigned positive charge : 363.7628 centred at (gu) : 87.27810 94.62829 86.04755 assigned negative charge : -362.7495 centred at (gu) : 87.73708 94.61187 85.93260 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 90570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21965 grid for indexing accessible points = 1.400000 m= 37841 mr = 63144 m= 8521 mr = 28623 m= 884 mr = 5848 m= 26 mr = 453 m= 0 mr = 5 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 410 time to turn everything in is 0.7100000 number of dielectric boundary points 39769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 18150 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) : 0.7116299 object centre at (A) : 8.844999 16.79800 61.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1773991E-02 2.8008133E-02 midg,1,midg; midg,igrid,midg -3.6315951E-03 -7.4767796E-03 1,midg,midg; igrid,midg,midg 3.2683007E-02 -2.0588350E-02 gauss-seidel spectral radius is 0.9988852 estimated iterations to convergence 237 setup time was (sec) 1.030000 now iterating at: 19:32:13 rms-change max change #iterations 5.152010 187.8171 at 10iterations 2.596480 84.40819 at 20iterations 1.307530 37.35675 at 30iterations 0.6576971 18.47969 at 40iterations 0.3326684 9.173960 at 50iterations 0.1678966 4.676414 at 60iterations 8.4388159E-02 2.375990 at 70iterations 4.2719308E-02 1.174696 at 80iterations 2.1787727E-02 0.6580620 at 90iterations 1.1111372E-02 0.3170652 at 100iterations 5.8050314E-03 0.1671143 at 110iterations 3.1356968E-03 8.8817596E-02 at 120iterations finished qdiffx linear iterations at : 19:32:19 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 3.1356968E-03 8.8817596E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 19:32:20 7.607u 0.243s 0:08.14 96.3% 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 19:32:20 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2418 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.202335 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): -14.63800 32.32800 ymin,ymax (A): -6.705000 40.30100 zmin,zma (A): 36.21900 86.24500 x,y,z range (A): 46.96600 47.00600 50.02600 scale (grids/A): 3.202335 object centre (A): 8.844999 16.79800 61.23200 number of atom coordinates read : 2418 total number of charged atoms : 2281 net assigned charge : 1.014006 assigned positive charge : 363.7628 centred at (gu) : 85.91705 96.94246 84.07117 assigned negative charge : -362.7495 centred at (gu) : 86.60562 96.91766 83.89895 start vw surface at 0.1500000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 208745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21965 grid for indexing accessible points = 1.400000 m= 114153 mr = 152232 m= 50657 mr = 94585 m= 16388 mr = 41833 m= 3672 mr = 12789 m= 462 mr = 2657 m= 23 mr = 306 m= 0 mr = 13 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 1278 time to turn everything in is 2.130000 number of dielectric boundary points 89685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 18244 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) : 2.134890 object centre at (A) : 8.844999 16.79800 61.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2190775 0.6331517 midg,1,midg; midg,igrid,midg -0.1572847 -5.2335910E-02 1,midg,midg; igrid,midg,midg 0.2049126 -0.2070329 gauss-seidel spectral radius is 0.9993232 estimated iterations to convergence 303 setup time was (sec) 2.460000 now iterating at: 19:32:23 rms-change max change #iterations 11.48396 357.9344 at 10iterations 6.889479 129.8226 at 20iterations 4.132977 76.80305 at 30iterations 2.466215 44.75097 at 40iterations 1.468629 24.24530 at 50iterations 0.8731765 15.80692 at 60iterations 0.5180514 8.550858 at 70iterations 0.3074690 5.407270 at 80iterations 0.1818007 2.861234 at 90iterations 0.1076253 1.737043 at 100iterations 6.3680761E-02 1.114042 at 110iterations 3.7652109E-02 0.6145020 at 120iterations 2.2373453E-02 0.3662910 at 130iterations 1.3366021E-02 0.2245235 at 140iterations 8.0681201E-03 0.1267071 at 150iterations 4.9955258E-03 8.3218575E-02 at 160iterations 3.2310479E-03 5.2692413E-02 at 170iterations 2.2234111E-03 3.8202286E-02 at 180iterations finished qdiffx linear iterations at : 19:32:35 total time elapsed so far: 14.85000 # loops : 180 mean,max change (kT/e) : 2.2234111E-03 3.8202286E-02 energy calculations done at 14.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.03000 DelPhi exited at 19:32:36 15.030u 0.270s 0:15.69 97.5% 0+0k 0+0io 0pf+0w