Mon Oct 10 19:34:45 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 19:34:46 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 !!! WARNING: HIT 106 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5773410 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): 1.317000 62.97900 ymin,ymax (A): 12.17400 58.86300 zmin,zma (A): -7.240000 40.34100 x,y,z range (A): 61.66200 46.68900 47.58101 scale (grids/A): 0.5773410 object centre (A): 32.14800 35.51850 16.55050 number of atom coordinates read : 2776 total number of charged atoms : 2637 net assigned charge : -3.485968 assigned positive charge : 416.8172 centred at (gu) : 89.43758 89.66164 89.55539 assigned negative charge : -420.3043 centred at (gu) : 89.41875 89.81883 89.48398 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6011 nv = 96 ne = 84 npr = 56090 no. pairs analyzed = 56090 no. exposed pairs = 3654 no. arc points = 25763 no. surface atoms = 1230 nbur = 1546 mkacc time = 0.1000000 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 = 1.512000 m= 259 mr = 3033 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2596 ## 280 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7741 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2945983E-09 5.8646499E-10 midg,1,midg; midg,igrid,midg 2.4390312E-09 -3.4571850E-09 1,midg,midg; igrid,midg,midg -1.2001077E-09 -2.9730846E-10 gauss-seidel spectral radius is 0.9845019 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 19:34:46 rms-change max change #iterations 9.2615344E-02 15.05933 at 10iterations 6.9906982E-03 1.033390 at 20iterations 5.3809216E-04 0.1100769 at 30iterations 4.3088643E-05 6.4792633E-03 at 40iterations 3.3430588E-06 5.2642822E-04 at 50iterations finished qdiffx linear iterations at : 19:34:49 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.3430588E-06 5.2642822E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 19:34:50 3.417u 0.173s 0:04.07 87.9% 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 Mon Oct 10 2011 at 19:34:50 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 !!! WARNING: HIT 106 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.732023 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): 1.317000 62.97900 ymin,ymax (A): 12.17400 58.86300 zmin,zma (A): -7.240000 40.34100 x,y,z range (A): 61.66200 46.68900 47.58101 scale (grids/A): 1.732023 object centre (A): 32.14800 35.51850 16.55050 number of atom coordinates read : 2776 total number of charged atoms : 2637 net assigned charge : -3.485968 assigned positive charge : 416.8172 centred at (gu) : 88.31183 88.98428 88.66549 assigned negative charge : -420.3043 centred at (gu) : 88.25579 89.45613 88.45166 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66547 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25763 grid for indexing accessible points = 1.400000 m= 20343 mr = 44560 m= 2205 mr = 13876 m= 59 mr = 1026 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 888 time to turn everything in is 0.3200000 number of dielectric boundary points 29688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20455 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) : 0.5773410 object centre at (A) : 32.14800 35.51850 16.55050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6619352E-03 -6.2476256E-04 midg,1,midg; midg,igrid,midg 1.2358862E-02 -2.0603577E-02 1,midg,midg; igrid,midg,midg -3.2446932E-03 -1.5615563E-02 gauss-seidel spectral radius is 0.9983734 estimated iterations to convergence 197 setup time was (sec) 0.5400000 now iterating at: 19:34:50 rms-change max change #iterations 3.625044 155.7075 at 10iterations 1.575546 57.05683 at 20iterations 0.6868959 25.88892 at 30iterations 0.2991402 10.72229 at 40iterations 0.1302921 4.909480 at 50iterations 5.6884028E-02 2.178396 at 60iterations 2.4945855E-02 0.8764722 at 70iterations 1.0843444E-02 0.3594694 at 80iterations 4.7442135E-03 0.1718826 at 90iterations 2.0747737E-03 7.3030949E-02 at 100iterations 9.0631651E-04 3.0538678E-02 at 110iterations 3.9505717E-04 1.2504578E-02 at 120iterations finished qdiffx linear iterations at : 19:34:57 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 3.9505717E-04 1.2504578E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 19:34:58 7.742u 0.199s 0:08.42 94.1% 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 19:34:58 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 !!! WARNING: HIT 106 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.598034 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): 1.317000 62.97900 ymin,ymax (A): 12.17400 58.86300 zmin,zma (A): -7.240000 40.34100 x,y,z range (A): 61.66200 46.68900 47.58101 scale (grids/A): 2.598034 object centre (A): 32.14800 35.51850 16.55050 number of atom coordinates read : 2776 total number of charged atoms : 2637 net assigned charge : -3.485968 assigned positive charge : 416.8172 centred at (gu) : 87.46752 88.47619 87.99792 assigned negative charge : -420.3043 centred at (gu) : 87.38355 89.18420 87.67757 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 154277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25763 grid for indexing accessible points = 1.400000 m= 70161 mr = 108773 m= 20236 mr = 55185 m= 3351 mr = 15080 m= 252 mr = 2123 m= 7 mr = 101 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 3039 time to turn everything in is 0.8100000 number of dielectric boundary points 67023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 21091 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) : 1.732023 object centre at (A) : 32.14800 35.51850 16.55050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2472826E-02 -1.6444001E-02 midg,1,midg; midg,igrid,midg 0.1926551 -0.2392970 1,midg,midg; igrid,midg,midg 3.6109794E-02 -0.2424383 gauss-seidel spectral radius is 0.9991961 estimated iterations to convergence 278 setup time was (sec) 1.050000 now iterating at: 19:34:59 rms-change max change #iterations 9.161984 283.0252 at 10iterations 5.246777 144.9071 at 20iterations 2.978107 68.17888 at 30iterations 1.686919 44.24340 at 40iterations 0.9542403 21.73341 at 50iterations 0.5388360 11.36026 at 60iterations 0.3023958 6.464408 at 70iterations 0.1704222 3.345284 at 80iterations 9.5745504E-02 1.909471 at 90iterations 5.3721920E-02 1.176164 at 100iterations 3.0161396E-02 0.6245451 at 110iterations 1.6922213E-02 0.3321648 at 120iterations 9.4962725E-03 0.2081909 at 130iterations 5.3150528E-03 0.1045113 at 140iterations 2.9817263E-03 6.1058044E-02 at 150iterations 1.6757499E-03 3.2867432E-02 at 160iterations 9.3713973E-04 1.8202782E-02 at 170iterations 5.2604731E-04 1.0488510E-02 at 180iterations finished qdiffx linear iterations at : 19:35:11 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 5.2604731E-04 1.0488510E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 19:35:11 12.367u 0.194s 0:13.03 96.3% 0+0k 0+0io 0pf+0w