Wed Dec 21 14:21:28 PST 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 Wed Dec 21 2011 at 14:21:28 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 = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6543636 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): -6.329000 34.24800 ymin,ymax (A): -3.422000 48.88900 zmin,zma (A): -23.51000 30.89400 x,y,z range (A): 40.57700 52.31100 54.40400 scale (grids/A): 0.6543636 object centre (A): 13.95950 22.73350 3.692000 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 91.03239 92.36632 89.97775 assigned negative charge : -284.4403 centred at (gu) : 91.14873 92.52854 89.90903 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5697 nv = 96 ne = 84 npr = 40486 no. pairs analyzed = 40486 no. exposed pairs = 2437 no. arc points = 17064 no. surface atoms = 818 nbur = 1148 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 3209 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2500000 number of dielectric boundary points 2765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1736 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9462857E-10 1.6416088E-08 midg,1,midg; midg,igrid,midg 1.7024384E-08 -2.1267619E-08 1,midg,midg; igrid,midg,midg 1.7974338E-08 -8.3918552E-09 gauss-seidel spectral radius is 0.9878384 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 14:21:29 rms-change max change #iterations 0.1361353 26.20319 at 10iterations 1.4521371E-02 2.029572 at 20iterations 1.4855932E-03 0.2449493 at 30iterations 1.5107826E-04 2.4011135E-02 at 40iterations 1.5995620E-05 2.4871826E-03 at 50iterations finished qdiffx linear iterations at : 14:21:33 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 1.5995620E-05 2.4871826E-03 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 14:21:35 4.506u 0.438s 0:07.62 64.6% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:36 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 = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.963091 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): -6.329000 34.24800 ymin,ymax (A): -3.422000 48.88900 zmin,zma (A): -23.51000 30.89400 x,y,z range (A): 40.57700 52.31100 54.40400 scale (grids/A): 1.963091 object centre (A): 13.95950 22.73350 3.692000 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 93.09718 97.09921 89.93328 assigned negative charge : -284.4403 centred at (gu) : 93.44644 97.58590 89.72756 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 61459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17064 grid for indexing accessible points = 1.400000 m= 22500 mr = 42701 m= 3520 mr = 17149 m= 190 mr = 2337 m= 0 mr = 58 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2180 time to turn everything in is 0.6200000 number of dielectric boundary points 25424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 14482 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) : 0.6543636 object centre at (A) : 13.95950 22.73350 3.692000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7303235E-02 1.9241255E-02 midg,1,midg; midg,igrid,midg 3.9869748E-02 -1.2162812E-02 1,midg,midg; igrid,midg,midg 1.2399895E-02 -3.7648582E-03 gauss-seidel spectral radius is 0.9986328 estimated iterations to convergence 214 setup time was (sec) 1.170000 now iterating at: 14:21:38 rms-change max change #iterations 3.732352 166.3472 at 10iterations 1.754907 62.64787 at 20iterations 0.8200973 29.27283 at 30iterations 0.3828403 12.56998 at 40iterations 0.1788499 5.801775 at 50iterations 8.3972067E-02 2.755797 at 60iterations 3.9198089E-02 1.343124 at 70iterations 1.8354241E-02 0.6369781 at 80iterations 8.5873231E-03 0.2836647 at 90iterations 4.0071281E-03 0.1344695 at 100iterations 1.8797461E-03 6.9053650E-02 at 110iterations 8.7986444E-04 3.0273438E-02 at 120iterations finished qdiffx linear iterations at : 14:21:52 total time elapsed so far: 14.41000 # loops : 120 mean,max change (kT/e) : 8.7986444E-04 3.0273438E-02 energy calculations done at 14.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.58000 DelPhi exited at 14:21:57 14.587u 0.894s 0:21.44 72.1% 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 Wed Dec 21 2011 at 14:21:59 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 = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.944636 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): -6.329000 34.24800 ymin,ymax (A): -3.422000 48.88900 zmin,zma (A): -23.51000 30.89400 x,y,z range (A): 40.57700 52.31100 54.40400 scale (grids/A): 2.944636 object centre (A): 13.95950 22.73350 3.692000 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 94.64573 100.6488 89.90002 assigned negative charge : -284.4403 centred at (gu) : 95.16982 101.3790 89.59129 start vw surface at 0.1100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 141726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17064 grid for indexing accessible points = 1.400000 m= 72603 mr = 102914 m= 26951 mr = 60467 m= 6568 mr = 22390 m= 914 mr = 5102 m= 41 mr = 599 m= 0 mr = 15 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 7116 time to turn everything in is 1.330000 number of dielectric boundary points 57316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 14656 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) : 1.963091 object centre at (A) : 13.95950 22.73350 3.692000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7945946 7.4002400E-02 midg,1,midg; midg,igrid,midg 0.3736311 -0.1579614 1,midg,midg; igrid,midg,midg 9.0369269E-02 -1.0789066E-02 gauss-seidel spectral radius is 0.9992462 estimated iterations to convergence 287 setup time was (sec) 1.650000 now iterating at: 14:22:02 rms-change max change #iterations 8.675523 428.1133 at 10iterations 4.979477 133.1261 at 20iterations 2.836373 60.61214 at 30iterations 1.619819 32.98146 at 40iterations 0.9265708 21.92903 at 50iterations 0.5274531 10.04053 at 60iterations 0.3007046 5.816430 at 70iterations 0.1712652 3.400793 at 80iterations 9.7796373E-02 1.881675 at 90iterations 5.5700857E-02 1.066542 at 100iterations 3.1707846E-02 0.6184549 at 110iterations 1.8141795E-02 0.3671994 at 120iterations 1.0327950E-02 0.2074451 at 130iterations 5.8905003E-03 0.1275482 at 140iterations 3.3566898E-03 7.4817657E-02 at 150iterations 1.9187389E-03 3.7597656E-02 at 160iterations 1.0941854E-03 2.0513535E-02 at 170iterations 6.2274630E-04 1.2293696E-02 at 180iterations finished qdiffx linear iterations at : 14:22:28 total time elapsed so far: 27.44000 # loops : 180 mean,max change (kT/e) : 6.2274630E-04 1.2293696E-02 energy calculations done at 27.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 27.63000 DelPhi exited at 14:22:33 27.636u 0.569s 0:33.97 82.9% 0+0k 0+0io 0pf+0w