Sat Oct 15 13:46:31 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 Sat Oct 15 2011 at 13:46:31 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2276 !!! WARNING: GLM 55 has a net charge of -0.0940 !!! WARNING: SEP 89 has a net charge of -0.4750 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: 0.6392645 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): -5.897000 41.05800 ymin,ymax (A): 15.83600 71.52500 zmin,zma (A): -0.4499999 47.80300 x,y,z range (A): 46.95500 55.68900 48.25300 scale (grids/A): 0.6392645 object centre (A): 17.58050 43.68050 23.67650 number of atom coordinates read : 2276 total number of charged atoms : 2193 net assigned charge : -3.568999 assigned positive charge : 334.6163 centred at (gu) : 89.93823 89.82092 88.26945 assigned negative charge : -338.1859 centred at (gu) : 89.98564 89.85510 88.20522 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6293 nv = 96 ne = 84 npr = 45955 no. pairs analyzed = 45955 no. exposed pairs = 3047 no. arc points = 20914 no. surface atoms = 1037 nbur = 1239 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3322 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1900000 number of dielectric boundary points 3293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2053 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7635 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6523581E-08 8.7818980E-10 midg,1,midg; midg,igrid,midg -1.6238666E-09 -8.0521785E-09 1,midg,midg; igrid,midg,midg -2.7084970E-10 -9.5609023E-09 gauss-seidel spectral radius is 0.9872967 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 13:46:32 rms-change max change #iterations 0.1357303 23.35574 at 10iterations 1.3184305E-02 1.879326 at 20iterations 1.3172932E-03 0.1897907 at 30iterations 1.4585583E-04 2.1166772E-02 at 40iterations 2.3565535E-05 3.3674240E-03 at 50iterations finished qdiffx linear iterations at : 13:46:38 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 2.3565535E-05 3.3674240E-03 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 13:46:39 3.951u 0.250s 0:07.76 54.1% 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 Sat Oct 15 2011 at 13:46:39 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2276 !!! WARNING: GLM 55 has a net charge of -0.0940 !!! WARNING: SEP 89 has a net charge of -0.4750 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: 1.917793 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): -5.897000 41.05800 ymin,ymax (A): 15.83600 71.52500 zmin,zma (A): -0.4499999 47.80300 x,y,z range (A): 46.95500 55.68900 48.25300 scale (grids/A): 1.917793 object centre (A): 17.58050 43.68050 23.67650 number of atom coordinates read : 2276 total number of charged atoms : 2193 net assigned charge : -3.568999 assigned positive charge : 334.6163 centred at (gu) : 89.81432 89.46245 84.80792 assigned negative charge : -338.1859 centred at (gu) : 89.95671 89.56532 84.61568 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20914 grid for indexing accessible points = 1.400000 m= 24235 mr = 46156 m= 4088 mr = 17343 m= 278 mr = 2510 m= 5 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 876 time to turn everything in is 0.3600000 number of dielectric boundary points 30289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 17262 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) : 0.6392645 object centre at (A) : 17.58050 43.68050 23.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3392429E-02 8.1076752E-03 midg,1,midg; midg,igrid,midg 2.7028091E-02 -4.2418959E-03 1,midg,midg; igrid,midg,midg -4.9452321E-03 -2.4824582E-02 gauss-seidel spectral radius is 0.9986277 estimated iterations to convergence 214 setup time was (sec) 0.6300000 now iterating at: 13:46:41 rms-change max change #iterations 3.977067 159.7060 at 10iterations 1.858893 62.56670 at 20iterations 0.8739464 32.37093 at 30iterations 0.4087552 14.46729 at 40iterations 0.1907445 6.687683 at 50iterations 8.9295879E-02 3.159958 at 60iterations 4.1761007E-02 1.350050 at 70iterations 1.9551538E-02 0.6963109 at 80iterations 9.1760075E-03 0.3055429 at 90iterations 4.2894324E-03 0.1475506 at 100iterations 2.0123268E-03 6.8503380E-02 at 110iterations 9.3889394E-04 3.0218124E-02 at 120iterations finished qdiffx linear iterations at : 13:46:52 total time elapsed so far: 8.660000 # loops : 120 mean,max change (kT/e) : 9.3889394E-04 3.0218124E-02 energy calculations done at 8.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 13:46:52 8.789u 0.304s 0:12.94 70.1% 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 Sat Oct 15 2011 at 13:46:53 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2276 !!! WARNING: GLM 55 has a net charge of -0.0940 !!! WARNING: SEP 89 has a net charge of -0.4750 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: 2.876690 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): -5.897000 41.05800 ymin,ymax (A): 15.83600 71.52500 zmin,zma (A): -0.4499999 47.80300 x,y,z range (A): 46.95500 55.68900 48.25300 scale (grids/A): 2.876690 object centre (A): 17.58050 43.68050 23.67650 number of atom coordinates read : 2276 total number of charged atoms : 2193 net assigned charge : -3.568999 assigned positive charge : 334.6163 centred at (gu) : 89.72131 89.19351 82.21194 assigned negative charge : -338.1859 centred at (gu) : 89.93506 89.34789 81.92343 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 156738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20914 grid for indexing accessible points = 1.400000 m= 77271 mr = 112052 m= 28730 mr = 62059 m= 7297 mr = 22695 m= 1219 mr = 5415 m= 98 mr = 811 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2956 time to turn everything in is 0.9200000 number of dielectric boundary points 68273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 17536 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) : 1.917793 object centre at (A) : 17.58050 43.68050 23.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3615437 0.1281794 midg,1,midg; midg,igrid,midg 0.3427374 -1.0029404E-02 1,midg,midg; igrid,midg,midg -5.4816388E-02 -0.2231112 gauss-seidel spectral radius is 0.9992559 estimated iterations to convergence 289 setup time was (sec) 1.210000 now iterating at: 13:46:54 rms-change max change #iterations 9.339580 487.5592 at 10iterations 5.456426 126.7979 at 20iterations 3.182609 64.31207 at 30iterations 1.843345 40.59819 at 40iterations 1.069382 23.53576 at 50iterations 0.6182130 12.43574 at 60iterations 0.3561627 7.052713 at 70iterations 0.2056625 4.333000 at 80iterations 0.1184141 2.478669 at 90iterations 6.8078600E-02 1.331001 at 100iterations 3.9338324E-02 0.8365040 at 110iterations 2.2508705E-02 0.4070203 at 120iterations 1.2943208E-02 0.2536581 at 130iterations 7.4311718E-03 0.1738129 at 140iterations 4.2729429E-03 0.1012480 at 150iterations 2.4526643E-03 4.7250748E-02 at 160iterations 1.4095191E-03 2.8116703E-02 at 170iterations 8.0814189E-04 1.4708996E-02 at 180iterations finished qdiffx linear iterations at : 13:47:18 total time elapsed so far: 14.58000 # loops : 180 mean,max change (kT/e) : 8.0814189E-04 1.4708996E-02 energy calculations done at 14.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.71000 DelPhi exited at 13:47:19 14.714u 0.336s 0:26.39 56.9% 0+0k 0+0io 0pf+0w