Sun Oct 9 03:34:11 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 Sun Oct 9 2011 at 03:34:11 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4567 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 4 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4205254 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): -3.394000 54.34400 ymin,ymax (A): -84.88800 -18.07900 zmin,zma (A): -14.33700 70.31900 x,y,z range (A): 57.73800 66.80900 84.65600 scale (grids/A): 0.4205254 object centre (A): 25.47500 -51.48350 27.99100 number of atom coordinates read : 4567 total number of charged atoms : 4380 net assigned charge : 19.99999 assigned positive charge : 676.5280 centred at (gu) : 89.73679 88.16470 93.65897 assigned negative charge : -656.5329 centred at (gu) : 89.71143 88.16448 93.71332 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 4895 nv = 96 ne = 84 npr = 90125 no. pairs analyzed = 90125 no. exposed pairs = 5938 no. arc points = 41311 no. surface atoms = 2008 nbur = 2559 mkacc time = 0.1900000 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 = 2.016000 m= 129 mr = 2293 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 2731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3265 ## 714 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 6631 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0956904E-12 3.0129523E-12 midg,1,midg; midg,igrid,midg 3.8704174E-12 1.2529770E-12 1,midg,midg; igrid,midg,midg 1.7754527E-12 2.5205658E-12 gauss-seidel spectral radius is 0.9711930 estimated iterations to convergence 49 setup time was (sec) 0.6500000 now iterating at: 03:34:12 rms-change max change #iterations 2.5577586E-02 5.308947 at 10iterations 3.3000109E-03 0.5817127 at 20iterations 8.8295486E-04 0.1705017 at 30iterations 2.4599329E-04 4.9036026E-02 at 40iterations 6.9136018E-05 1.3959885E-02 at 50iterations finished qdiffx linear iterations at : 03:34:14 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 6.9136018E-05 1.3959885E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 03:34:15 3.461u 0.178s 0:03.91 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 Sun Oct 9 2011 at 03:34:15 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4567 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 4 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.261576 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): -3.394000 54.34400 ymin,ymax (A): -84.88800 -18.07900 zmin,zma (A): -14.33700 70.31900 x,y,z range (A): 57.73800 66.80900 84.65600 scale (grids/A): 1.261576 object centre (A): 25.47500 -51.48350 27.99100 number of atom coordinates read : 4567 total number of charged atoms : 4380 net assigned charge : 19.99999 assigned positive charge : 676.5280 centred at (gu) : 89.20850 84.49266 100.9754 assigned negative charge : -656.5329 centred at (gu) : 89.13412 84.49296 101.1397 start vw surface at 0.1800000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 57712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41311 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 13079 mr = 37755 m= 594 mr = 7698 m= 4 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.4500000 number of dielectric boundary points 25846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 745 ## 31 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 30121 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) : 0.4205254 object centre at (A) : 25.47500 -51.48350 27.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6545343E-03 1.5374249E-02 midg,1,midg; midg,igrid,midg 3.7497045E-03 1.8599188E-03 1,midg,midg; igrid,midg,midg 1.2039999E-03 1.0194260E-03 gauss-seidel spectral radius is 0.9970422 estimated iterations to convergence 147 setup time was (sec) 0.7400000 now iterating at: 03:34:16 rms-change max change #iterations 2.234818 107.1062 at 10iterations 0.7312608 34.88275 at 20iterations 0.2408924 9.416265 at 30iterations 7.9681873E-02 3.605739 at 40iterations 2.6793415E-02 1.143757 at 50iterations 9.5588779E-03 0.4624329 at 60iterations 3.9474173E-03 0.1839523 at 70iterations 2.0023985E-03 9.0957642E-02 at 80iterations 1.1989245E-03 5.2833557E-02 at 90iterations 7.6022802E-04 3.2985687E-02 at 100iterations 4.9269100E-04 2.1619797E-02 at 110iterations 3.2190996E-04 1.4219284E-02 at 120iterations finished qdiffx linear iterations at : 03:34:22 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 3.2190996E-04 1.4219284E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 03:34:23 7.573u 0.242s 0:08.10 96.4% 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 Sun Oct 9 2011 at 03:34:23 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4567 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 4 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.892364 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): -3.394000 54.34400 ymin,ymax (A): -84.88800 -18.07900 zmin,zma (A): -14.33700 70.31900 x,y,z range (A): 57.73800 66.80900 84.65600 scale (grids/A): 1.892364 object centre (A): 25.47500 -51.48350 27.99100 number of atom coordinates read : 4567 total number of charged atoms : 4380 net assigned charge : 19.99999 assigned positive charge : 676.5280 centred at (gu) : 88.81249 81.73852 106.4627 assigned negative charge : -656.5329 centred at (gu) : 88.70106 81.73954 106.7095 start vw surface at 0.1800000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 135732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41311 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 51140 mr = 94624 m= 8751 mr = 37543 m= 552 mr = 5392 m= 6 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 1.000000 number of dielectric boundary points 58444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 34452 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) : 1.261576 object centre at (A) : 25.47500 -51.48350 27.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0658257E-02 0.4233078 midg,1,midg; midg,igrid,midg 0.1033389 5.0774675E-02 1,midg,midg; igrid,midg,midg 3.0185321E-02 2.5627231E-02 gauss-seidel spectral radius is 0.9987803 estimated iterations to convergence 227 setup time was (sec) 1.310000 now iterating at: 03:34:24 rms-change max change #iterations 6.903260 218.2286 at 10iterations 3.498801 100.1450 at 20iterations 1.762828 56.51245 at 30iterations 0.8814497 23.27879 at 40iterations 0.4387786 12.68257 at 50iterations 0.2181252 6.555029 at 60iterations 0.1077425 2.697939 at 70iterations 5.3276602E-02 1.317158 at 80iterations 2.6316447E-02 0.7286873 at 90iterations 1.2991348E-02 0.3288975 at 100iterations 6.4589935E-03 0.1777868 at 110iterations 3.2429073E-03 8.3932877E-02 at 120iterations 1.6589225E-03 4.3796539E-02 at 130iterations 8.8603626E-04 2.4868011E-02 at 140iterations 5.0175155E-04 1.4152527E-02 at 150iterations 3.0844862E-04 8.2054138E-03 at 160iterations 2.0455220E-04 5.5847168E-03 at 170iterations 1.4311090E-04 3.6869049E-03 at 180iterations finished qdiffx linear iterations at : 03:34:35 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 1.4311090E-04 3.6869049E-03 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 03:34:36 12.183u 0.223s 0:12.73 97.4% 0+0k 0+0io 0pf+0w