Sat Oct 8 14:46:06 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 Sat Oct 8 2011 at 14:46:06 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6378099 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): -12.27200 43.54400 ymin,ymax (A): -22.88800 22.32700 zmin,zma (A): -6.589000 47.55900 x,y,z range (A): 55.81600 45.21500 54.14800 scale (grids/A): 0.6378099 object centre (A): 15.63600 -0.2805004 20.48500 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : -1.999993 assigned positive charge : 452.5276 centred at (gu) : 88.89981 89.83389 91.30183 assigned negative charge : -454.5283 centred at (gu) : 88.85561 89.73615 91.26560 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8203 nv = 96 ne = 84 npr = 63169 no. pairs analyzed = 63169 no. exposed pairs = 3431 no. arc points = 24178 no. surface atoms = 1171 nbur = 1858 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 4788 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2300000 number of dielectric boundary points 3807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2313 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9921 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5768532E-09 2.6385765E-09 midg,1,midg; midg,igrid,midg -1.5931818E-08 9.3633998E-09 1,midg,midg; igrid,midg,midg -1.0648519E-08 2.2957736E-09 gauss-seidel spectral radius is 0.9872982 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 14:46:07 rms-change max change #iterations 0.1552173 23.46363 at 10iterations 1.5229193E-02 2.225633 at 20iterations 1.5516429E-03 0.1885552 at 30iterations 1.6226077E-04 1.9697189E-02 at 40iterations 2.0421425E-05 2.5978088E-03 at 50iterations finished qdiffx linear iterations at : 14:46:10 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 2.0421425E-05 2.5978088E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 14:46:10 3.670u 0.209s 0:04.15 93.2% 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 Sat Oct 8 2011 at 14:46:10 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.913430 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): -12.27200 43.54400 ymin,ymax (A): -22.88800 22.32700 zmin,zma (A): -6.589000 47.55900 x,y,z range (A): 55.81600 45.21500 54.14800 scale (grids/A): 1.913430 object centre (A): 15.63600 -0.2805004 20.48500 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : -1.999993 assigned positive charge : 452.5276 centred at (gu) : 86.69853 89.50107 93.90501 assigned negative charge : -454.5283 centred at (gu) : 86.56636 89.20830 93.79645 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 89934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24178 grid for indexing accessible points = 1.400000 m= 32662 mr = 65086 m= 4785 mr = 24492 m= 286 mr = 2897 m= 2 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 592 time to turn everything in is 0.4500000 number of dielectric boundary points 35093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 22706 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) : 0.6378099 object centre at (A) : 15.63600 -0.2805004 20.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2160803E-02 3.8583404E-03 midg,1,midg; midg,igrid,midg -7.6155867E-03 1.6955830E-02 1,midg,midg; igrid,midg,midg -4.0326629E-02 1.2924780E-02 gauss-seidel spectral radius is 0.9986840 estimated iterations to convergence 218 setup time was (sec) 0.7200000 now iterating at: 14:46:11 rms-change max change #iterations 4.681571 210.4836 at 10iterations 2.233562 66.47771 at 20iterations 1.060215 31.33961 at 30iterations 0.5044901 16.09043 at 40iterations 0.2397091 6.780082 at 50iterations 0.1140708 3.197181 at 60iterations 5.4428186E-02 1.527648 at 70iterations 2.5770206E-02 0.7275753 at 80iterations 1.2300989E-02 0.3736839 at 90iterations 5.8363010E-03 0.1783600 at 100iterations 2.7905921E-03 9.1295242E-02 at 110iterations 1.3292335E-03 3.5339355E-02 at 120iterations finished qdiffx linear iterations at : 14:46:19 total time elapsed so far: 8.760000 # loops : 120 mean,max change (kT/e) : 1.3292335E-03 3.5339355E-02 energy calculations done at 8.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.930000 DelPhi exited at 14:46:20 8.930u 0.262s 0:09.49 96.8% 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 14:46:20 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.870145 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): -12.27200 43.54400 ymin,ymax (A): -22.88800 22.32700 zmin,zma (A): -6.589000 47.55900 x,y,z range (A): 55.81600 45.21500 54.14800 scale (grids/A): 2.870145 object centre (A): 15.63600 -0.2805004 20.48500 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : -1.999993 assigned positive charge : 452.5276 centred at (gu) : 85.04755 89.25141 95.85747 assigned negative charge : -454.5283 centred at (gu) : 84.84952 88.81240 95.69469 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 208088 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24178 grid for indexing accessible points = 1.400000 m= 107364 mr = 156815 m= 37888 mr = 89762 m= 8416 mr = 30425 m= 1175 mr = 6146 m= 65 mr = 742 m= 0 mr = 23 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 2091 time to turn everything in is 1.190000 number of dielectric boundary points 79083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 23054 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) : 1.913430 object centre at (A) : 15.63600 -0.2805004 20.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9947300E-02 0.1444371 midg,1,midg; midg,igrid,midg -6.2082402E-02 0.1937411 1,midg,midg; igrid,midg,midg -0.6052177 0.2100095 gauss-seidel spectral radius is 0.9992748 estimated iterations to convergence 293 setup time was (sec) 1.490000 now iterating at: 14:46:22 rms-change max change #iterations 10.94542 324.2784 at 10iterations 6.435806 149.7063 at 20iterations 3.756756 78.50842 at 30iterations 2.191006 41.32090 at 40iterations 1.274516 23.30910 at 50iterations 0.7416226 12.63572 at 60iterations 0.4312841 7.248040 at 70iterations 0.2497857 4.852883 at 80iterations 0.1445118 2.726659 at 90iterations 8.3986260E-02 1.348151 at 100iterations 4.8489712E-02 0.7976418 at 110iterations 2.8071128E-02 0.4611514 at 120iterations 1.6252557E-02 0.2789459 at 130iterations 9.4147744E-03 0.1557655 at 140iterations 5.4418403E-03 9.0171337E-02 at 150iterations 3.1454617E-03 5.9692383E-02 at 160iterations 1.8223765E-03 2.8717518E-02 at 170iterations 1.0538144E-03 1.7169952E-02 at 180iterations finished qdiffx linear iterations at : 14:46:35 total time elapsed so far: 14.44000 # loops : 180 mean,max change (kT/e) : 1.0538144E-03 1.7169952E-02 energy calculations done at 14.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.57000 DelPhi exited at 14:46:35 14.574u 0.279s 0:15.15 97.9% 0+0k 0+0io 0pf+0w