Sat Oct 8 13:21:46 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 13:21:46 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3666 !!! WARNING: TPO 306 has a net charge of -0.2260 !!! WARNING: GLU 656 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 !!! WARNING: TPO 2 has a net charge of -1.2740 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: 0.5786453 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): 7.683000 67.34700 ymin,ymax (A): -40.67800 20.84500 zmin,zma (A): -23.39100 28.82700 x,y,z range (A): 59.66400 61.52300 52.21800 scale (grids/A): 0.5786453 object centre (A): 37.51500 -9.916501 2.718000 number of atom coordinates read : 3666 total number of charged atoms : 3519 net assigned charge : 2.726033 assigned positive charge : 554.5070 centred at (gu) : 90.64069 89.09136 89.81537 assigned negative charge : -551.7828 centred at (gu) : 90.76542 89.20608 89.76941 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8218 nv = 96 ne = 84 npr = 72468 no. pairs analyzed = 72468 no. exposed pairs = 4824 no. arc points = 34158 no. surface atoms = 1604 nbur = 2062 mkacc time = 0.1300000 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= 347 mr = 4282 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3498 ## 424 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 10464 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6949174E-10 1.6857172E-09 midg,1,midg; midg,igrid,midg 4.3725445E-09 -1.9842132E-09 1,midg,midg; igrid,midg,midg 3.2454102E-09 -3.1986138E-09 gauss-seidel spectral radius is 0.9846468 estimated iterations to convergence 66 setup time was (sec) 0.4600000 now iterating at: 13:21:47 rms-change max change #iterations 0.1111679 19.40029 at 10iterations 8.9720767E-03 1.225044 at 20iterations 1.5680128E-03 0.2939339 at 30iterations 6.9160882E-04 0.1402760 at 40iterations 3.3458884E-04 6.9042206E-02 at 50iterations finished qdiffx linear iterations at : 13:21:50 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 3.3458884E-04 6.9042206E-02 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 13:21:51 3.714u 0.213s 0:04.22 92.8% 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 13:21:51 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3666 !!! WARNING: TPO 306 has a net charge of -0.2260 !!! WARNING: GLU 656 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 !!! WARNING: TPO 2 has a net charge of -1.2740 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: 1.735936 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): 7.683000 67.34700 ymin,ymax (A): -40.67800 20.84500 zmin,zma (A): -23.39100 28.82700 x,y,z range (A): 59.66400 61.52300 52.21800 scale (grids/A): 1.735936 object centre (A): 37.51500 -9.916501 2.718000 number of atom coordinates read : 3666 total number of charged atoms : 3519 net assigned charge : 2.726033 assigned positive charge : 554.5070 centred at (gu) : 91.92115 87.27309 89.44510 assigned negative charge : -551.7828 centred at (gu) : 92.29610 87.61778 89.30785 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 90115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34158 grid for indexing accessible points = 1.400000 m= 29714 mr = 61329 m= 3686 mr = 20907 m= 138 mr = 1996 m= 4 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 290 time to turn everything in is 0.4400000 number of dielectric boundary points 39406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 369 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 27298 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) : 0.5786453 object centre at (A) : 37.51500 -9.916501 2.718000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3878121E-03 3.3992622E-03 midg,1,midg; midg,igrid,midg 2.5607681E-02 -4.6081347E-03 1,midg,midg; igrid,midg,midg 4.4374589E-02 4.1413317E-03 gauss-seidel spectral radius is 0.9984831 estimated iterations to convergence 204 setup time was (sec) 0.6800000 now iterating at: 13:21:51 rms-change max change #iterations 4.336777 163.7669 at 10iterations 1.940876 62.46593 at 20iterations 0.8709512 26.56828 at 30iterations 0.3921171 11.70740 at 40iterations 0.1763811 6.379967 at 50iterations 7.9375662E-02 2.294334 at 60iterations 3.5943884E-02 1.107960 at 70iterations 1.6424580E-02 0.5140133 at 80iterations 7.6661278E-03 0.2396183 at 90iterations 3.8029384E-03 0.1413231 at 100iterations 2.1059804E-03 8.5534096E-02 at 110iterations 1.3336865E-03 5.2631378E-02 at 120iterations finished qdiffx linear iterations at : 13:21:59 total time elapsed so far: 8.170000 # loops : 120 mean,max change (kT/e) : 1.3336865E-03 5.2631378E-02 energy calculations done at 8.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 13:21:59 8.304u 0.220s 0:08.82 96.5% 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 13:21:59 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3666 !!! WARNING: TPO 306 has a net charge of -0.2260 !!! WARNING: GLU 656 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 !!! WARNING: TPO 2 has a net charge of -1.2740 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: 2.603904 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): 7.683000 67.34700 ymin,ymax (A): -40.67800 20.84500 zmin,zma (A): -23.39100 28.82700 x,y,z range (A): 59.66400 61.52300 52.21800 scale (grids/A): 2.603904 object centre (A): 37.51500 -9.916501 2.718000 number of atom coordinates read : 3666 total number of charged atoms : 3519 net assigned charge : 2.726033 assigned positive charge : 554.5070 centred at (gu) : 92.88154 85.90937 89.16736 assigned negative charge : -551.7828 centred at (gu) : 93.44402 86.42655 88.96155 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 208671 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34158 grid for indexing accessible points = 1.400000 m= 99879 mr = 149372 m= 31585 mr = 79871 m= 6202 mr = 24346 m= 659 mr = 4317 m= 28 mr = 348 m= 0 mr = 1 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1210 time to turn everything in is 1.130000 number of dielectric boundary points 88769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 28117 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) : 1.735936 object centre at (A) : 37.51500 -9.916501 2.718000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9448826E-02 -4.3359455E-02 midg,1,midg; midg,igrid,midg 0.3532814 -0.1316077 1,midg,midg; igrid,midg,midg 0.5896479 8.4299557E-02 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 1.420000 now iterating at: 13:22:01 rms-change max change #iterations 10.83592 394.5533 at 10iterations 6.383870 153.4166 at 20iterations 3.743701 79.81691 at 30iterations 2.181177 47.35332 at 40iterations 1.268192 27.62116 at 50iterations 0.7356017 14.17108 at 60iterations 0.4260849 8.567870 at 70iterations 0.2464003 4.681960 at 80iterations 0.1423105 2.999475 at 90iterations 8.2024634E-02 1.533232 at 100iterations 4.7336563E-02 0.8809571 at 110iterations 2.7274799E-02 0.5066204 at 120iterations 1.5725812E-02 0.2825933 at 130iterations 9.1072442E-03 0.1899071 at 140iterations 5.3260205E-03 0.1063232 at 150iterations 3.1580282E-03 6.2587738E-02 at 160iterations 1.9293502E-03 4.2675018E-02 at 170iterations 1.2425345E-03 2.7671814E-02 at 180iterations finished qdiffx linear iterations at : 13:22:14 total time elapsed so far: 14.13000 # loops : 180 mean,max change (kT/e) : 1.2425345E-03 2.7671814E-02 energy calculations done at 14.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.27000 DelPhi exited at 13:22:14 14.271u 0.255s 0:14.94 97.1% 0+0k 0+0io 0pf+0w