Sun Oct 9 16:40:55 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 Sun Oct 9 2011 at 16:40:55 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3149 !!! WARNING: GLU 251 has a net charge of -0.7280 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: 0.5689537 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): -51.10500 1.789000 ymin,ymax (A): 1.644000 64.21500 zmin,zma (A): -19.77600 40.88600 x,y,z range (A): 52.89400 62.57100 60.66199 scale (grids/A): 0.5689537 object centre (A): -24.65800 32.92950 10.55500 number of atom coordinates read : 3149 total number of charged atoms : 3002 net assigned charge : 0.7720084 assigned positive charge : 465.2719 centred at (gu) : 90.95909 91.54861 92.09261 assigned negative charge : -464.5015 centred at (gu) : 91.01711 91.52044 92.13408 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6839 nv = 96 ne = 84 npr = 61808 no. pairs analyzed = 61808 no. exposed pairs = 4331 no. arc points = 31001 no. surface atoms = 1460 nbur = 1689 mkacc time = 0.1100000 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 = 1.484000 m= 298 mr = 3291 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2200000 number of dielectric boundary points 3822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3109 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8639 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7294718E-10 -8.7956070E-10 midg,1,midg; midg,igrid,midg -2.1401915E-10 8.3120932E-10 1,midg,midg; igrid,midg,midg 8.2174778E-10 -9.9450703E-10 gauss-seidel spectral radius is 0.9840883 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 16:40:55 rms-change max change #iterations 9.0917282E-02 16.14143 at 10iterations 6.5818829E-03 1.000040 at 20iterations 5.0828315E-04 8.1635714E-02 at 30iterations 3.8605165E-05 6.0906410E-03 at 40iterations 3.8970429E-06 7.1907043E-04 at 50iterations finished qdiffx linear iterations at : 16:40:58 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.8970429E-06 7.1907043E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 16:40:59 3.474u 0.181s 0:03.98 91.7% 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 16:40:59 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3149 !!! WARNING: GLU 251 has a net charge of -0.7280 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: 1.706861 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): -51.10500 1.789000 ymin,ymax (A): 1.644000 64.21500 zmin,zma (A): -19.77600 40.88600 x,y,z range (A): 52.89400 62.57100 60.66199 scale (grids/A): 1.706861 object centre (A): -24.65800 32.92950 10.55500 number of atom coordinates read : 3149 total number of charged atoms : 3002 net assigned charge : 0.7720084 assigned positive charge : 465.2719 centred at (gu) : 92.87663 94.64487 96.27667 assigned negative charge : -464.5015 centred at (gu) : 93.05122 94.56129 96.40217 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74150 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31001 grid for indexing accessible points = 1.400000 m= 22923 mr = 47726 m= 2904 mr = 15473 m= 106 mr = 1704 m= 0 mr = 28 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 311 time to turn everything in is 0.3600000 number of dielectric boundary points 35152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 311 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 23211 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) : 0.5689537 object centre at (A) : -24.65800 32.92950 10.55500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3493792E-02 -4.5844372E-03 midg,1,midg; midg,igrid,midg -9.0956884E-03 -1.8946592E-02 1,midg,midg; igrid,midg,midg 6.1150719E-03 -7.2342772E-03 gauss-seidel spectral radius is 0.9983807 estimated iterations to convergence 197 setup time was (sec) 0.5800000 now iterating at: 16:41:00 rms-change max change #iterations 3.770813 195.2075 at 10iterations 1.636757 64.57001 at 20iterations 0.7129379 23.93495 at 30iterations 0.3116288 10.01179 at 40iterations 0.1361352 4.370749 at 50iterations 5.9651043E-02 2.049572 at 60iterations 2.6028242E-02 0.8732619 at 70iterations 1.1359369E-02 0.4144969 at 80iterations 4.9585905E-03 0.1902111 at 90iterations 2.1761407E-03 7.5559616E-02 at 100iterations 9.4980281E-04 3.5186768E-02 at 110iterations 4.1730382E-04 1.3416290E-02 at 120iterations finished qdiffx linear iterations at : 16:41:07 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 4.1730382E-04 1.3416290E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 16:41:07 7.935u 0.214s 0:08.46 96.2% 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 16:41:07 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3149 !!! WARNING: GLU 251 has a net charge of -0.7280 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: 2.560292 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): -51.10500 1.789000 ymin,ymax (A): 1.644000 64.21500 zmin,zma (A): -19.77600 40.88600 x,y,z range (A): 52.89400 62.57100 60.66199 scale (grids/A): 2.560292 object centre (A): -24.65800 32.92950 10.55500 number of atom coordinates read : 3149 total number of charged atoms : 3002 net assigned charge : 0.7720084 assigned positive charge : 465.2719 centred at (gu) : 94.31470 96.96693 99.41477 assigned negative charge : -464.5015 centred at (gu) : 94.57685 96.84197 99.60312 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 171857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31001 grid for indexing accessible points = 1.400000 m= 76779 mr = 117199 m= 23980 mr = 59603 m= 4878 mr = 18198 m= 508 mr = 3486 m= 14 mr = 342 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 1101 time to turn everything in is 0.9100000 number of dielectric boundary points 79188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 24001 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) : 1.706861 object centre at (A) : -24.65800 32.92950 10.55500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2106599 -0.1323949 midg,1,midg; midg,igrid,midg -0.1548776 -0.2898463 1,midg,midg; igrid,midg,midg 9.3513601E-02 -0.1035285 gauss-seidel spectral radius is 0.9992114 estimated iterations to convergence 281 setup time was (sec) 1.160000 now iterating at: 16:41:09 rms-change max change #iterations 9.453869 356.5250 at 10iterations 5.458859 138.9810 at 20iterations 3.134500 81.36040 at 30iterations 1.790226 43.52505 at 40iterations 1.020150 27.12458 at 50iterations 0.5803031 12.93790 at 60iterations 0.3290337 6.454346 at 70iterations 0.1865099 3.655560 at 80iterations 0.1052307 2.029533 at 90iterations 5.9567448E-02 1.323364 at 100iterations 3.3637825E-02 0.7194943 at 110iterations 1.9033989E-02 0.3703156 at 120iterations 1.0703598E-02 0.2073593 at 130iterations 6.0479762E-03 0.1187572 at 140iterations 3.4020767E-03 6.4765930E-02 at 150iterations 1.9199979E-03 3.5697937E-02 at 160iterations 1.0837584E-03 1.9782543E-02 at 170iterations 6.1095587E-04 1.1993527E-02 at 180iterations finished qdiffx linear iterations at : 16:41:20 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 6.1095587E-04 1.1993527E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 16:41:21 12.749u 0.213s 0:13.24 97.8% 0+0k 0+0io 0pf+0w