Sat Oct 15 13:43:19 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 15 2011 at 13:43:19 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5589663 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): 13.10600 73.70600 ymin,ymax (A): 128.8950 192.5840 zmin,zma (A): -7.094000 52.95200 x,y,z range (A): 60.60000 63.68900 60.04600 scale (grids/A): 0.5589663 object centre (A): 43.40600 160.7395 22.92900 number of atom coordinates read : 4072 total number of charged atoms : 3487 net assigned charge : 18.00000 assigned positive charge : 542.0445 centred at (gu) : 89.29520 89.69930 91.31461 assigned negative charge : -524.0460 centred at (gu) : 89.29906 89.86347 91.44467 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8434 nv = 96 ne = 84 npr = 81370 no. pairs analyzed = 81370 no. exposed pairs = 5884 no. arc points = 41102 no. surface atoms = 1950 nbur = 2122 mkacc time = 0.2100000 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 = 1.568000 m= 401 mr = 4012 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3483 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9655 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5329272E-09 2.3410177E-10 midg,1,midg; midg,igrid,midg 4.1697823E-09 -2.2251673E-10 1,midg,midg; igrid,midg,midg 2.2512936E-09 1.5344304E-09 gauss-seidel spectral radius is 0.9835934 estimated iterations to convergence 64 setup time was (sec) 0.7800000 now iterating at: 13:43:20 rms-change max change #iterations 9.2531987E-02 16.60463 at 10iterations 6.9296714E-03 1.014906 at 20iterations 9.4664318E-04 0.1378326 at 30iterations 3.1800891E-04 4.0380955E-02 at 40iterations 1.2099697E-04 1.5434742E-02 at 50iterations finished qdiffx linear iterations at : 13:43:25 total time elapsed so far: 5.330000 # loops : 50 mean,max change (kT/e) : 1.2099697E-04 1.5434742E-02 energy calculations done at 5.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.510000 DelPhi exited at 13:43:25 5.520u 0.476s 0:06.26 95.6% 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 15 2011 at 13:43:25 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.676899 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): 13.10600 73.70600 ymin,ymax (A): 128.8950 192.5840 zmin,zma (A): -7.094000 52.95200 x,y,z range (A): 60.60000 63.68900 60.04600 scale (grids/A): 1.676899 object centre (A): 43.40600 160.7395 22.92900 number of atom coordinates read : 4072 total number of charged atoms : 3487 net assigned charge : 18.00000 assigned positive charge : 542.0445 centred at (gu) : 87.88489 89.09700 93.94344 assigned negative charge : -524.0460 centred at (gu) : 87.89662 89.59013 94.33351 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 91725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41102 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29332 mr = 59156 m= 3506 mr = 19220 m= 108 mr = 1739 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 44543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 368 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 26799 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) : 0.5589663 object centre at (A) : 43.40600 160.7395 22.92900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7728461E-02 1.6361477E-02 midg,1,midg; midg,igrid,midg 5.2499752E-02 -9.5061306E-03 1,midg,midg; igrid,midg,midg 2.6856136E-02 2.0448809E-02 gauss-seidel spectral radius is 0.9984191 estimated iterations to convergence 200 setup time was (sec) 1.200000 now iterating at: 13:43:27 rms-change max change #iterations 3.951363 163.3729 at 10iterations 1.741691 65.26723 at 20iterations 0.7718896 29.24257 at 30iterations 0.3387129 12.52185 at 40iterations 0.1501648 4.536011 at 50iterations 6.6287734E-02 2.035542 at 60iterations 2.9383656E-02 0.9348891 at 70iterations 1.3012757E-02 0.3816566 at 80iterations 5.7822769E-03 0.1700211 at 90iterations 2.6104162E-03 8.1714630E-02 at 100iterations 1.2050299E-03 4.1837215E-02 at 110iterations 5.9266563E-04 1.7992020E-02 at 120iterations finished qdiffx linear iterations at : 13:43:40 total time elapsed so far: 13.59000 # loops : 120 mean,max change (kT/e) : 5.9266563E-04 1.7992020E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 13:43:40 13.746u 0.539s 0:14.73 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 15 2011 at 13:43:40 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.515348 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): 13.10600 73.70600 ymin,ymax (A): 128.8950 192.5840 zmin,zma (A): -7.094000 52.95200 x,y,z range (A): 60.60000 63.68900 60.04600 scale (grids/A): 2.515348 object centre (A): 43.40600 160.7395 22.92900 number of atom coordinates read : 4072 total number of charged atoms : 3487 net assigned charge : 18.00000 assigned positive charge : 542.0445 centred at (gu) : 86.82681 88.64507 95.91497 assigned negative charge : -524.0460 centred at (gu) : 86.84495 89.38529 96.50020 start vw surface at 0.1500000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 212453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41102 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 97964 mr = 145540 m= 30218 mr = 74573 m= 5628 mr = 22141 m= 483 mr = 3745 m= 11 mr = 211 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 100548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 27877 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) : 1.676899 object centre at (A) : 43.40600 160.7395 22.92900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3523997 0.3069851 midg,1,midg; midg,igrid,midg 0.6695042 -0.1868224 1,midg,midg; igrid,midg,midg 0.2186878 0.2161543 gauss-seidel spectral radius is 0.9992540 estimated iterations to convergence 289 setup time was (sec) 2.420000 now iterating at: 13:43:43 rms-change max change #iterations 10.27469 332.3711 at 10iterations 6.108007 150.6161 at 20iterations 3.599622 77.82052 at 30iterations 2.108744 45.06783 at 40iterations 1.230714 24.71535 at 50iterations 0.7159684 13.96985 at 60iterations 0.4151601 8.953981 at 70iterations 0.2405052 4.355474 at 80iterations 0.1387341 2.779606 at 90iterations 8.0089629E-02 1.383552 at 100iterations 4.6282597E-02 0.8530073 at 110iterations 2.6599577E-02 0.5223427 at 120iterations 1.5330620E-02 0.2976456 at 130iterations 8.8012032E-03 0.1571789 at 140iterations 5.0637852E-03 8.9239120E-02 at 150iterations 2.9074624E-03 5.6762695E-02 at 160iterations 1.6722542E-03 2.9771090E-02 at 170iterations 9.6093514E-04 1.7360687E-02 at 180iterations finished qdiffx linear iterations at : 13:44:10 total time elapsed so far: 22.77000 # loops : 180 mean,max change (kT/e) : 9.6093514E-04 1.7360687E-02 energy calculations done at 22.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.94000 DelPhi exited at 13:44:11 22.941u 0.582s 0:30.44 77.2% 0+0k 0+0io 0pf+0w