Sat Oct 15 14:42:12 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 14:42:12 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIT 148 has a net charge of 0.5140 !!! WARNING: PRO 352 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5315496 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): -18.69800 48.27600 ymin,ymax (A): -28.00600 19.74300 zmin,zma (A): -42.08000 8.813000 x,y,z range (A): 66.97400 47.74900 50.89300 scale (grids/A): 0.5315496 object centre (A): 14.78900 -4.131500 -16.63350 number of atom coordinates read : 3036 total number of charged atoms : 2895 net assigned charge : 1.4024414E-02 assigned positive charge : 456.5319 centred at (gu) : 88.88075 89.42172 88.98849 assigned negative charge : -456.5190 centred at (gu) : 88.88031 89.31197 88.86588 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5575 nv = 96 ne = 84 npr = 60005 no. pairs analyzed = 60005 no. exposed pairs = 4167 no. arc points = 29459 no. surface atoms = 1386 nbur = 1650 mkacc time = 0.1000000 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 = 1.624000 m= 218 mr = 2676 m= 0 mr = 9 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2940 ## 424 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2105709E-10 3.7111952E-10 midg,1,midg; midg,igrid,midg -4.9453069E-10 3.7248959E-10 1,midg,midg; igrid,midg,midg 1.0104898E-11 8.2812117E-12 gauss-seidel spectral radius is 0.9817753 estimated iterations to convergence 61 setup time was (sec) 0.4100000 now iterating at: 14:42:13 rms-change max change #iterations 6.2336963E-02 12.25971 at 10iterations 3.9754640E-03 0.7446215 at 20iterations 2.4410327E-04 3.8925171E-02 at 30iterations 1.5667500E-05 2.6035309E-03 at 40iterations 1.2265643E-06 2.4700165E-04 at 50iterations finished qdiffx linear iterations at : 14:42:18 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.2265643E-06 2.4700165E-04 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 14:42:19 3.592u 0.209s 0:06.78 55.8% 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 14:42:19 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIT 148 has a net charge of 0.5140 !!! WARNING: PRO 352 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.594649 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): -18.69800 48.27600 ymin,ymax (A): -28.00600 19.74300 zmin,zma (A): -42.08000 8.813000 x,y,z range (A): 66.97400 47.74900 50.89300 scale (grids/A): 1.594649 object centre (A): 14.78900 -4.131500 -16.63350 number of atom coordinates read : 3036 total number of charged atoms : 2895 net assigned charge : 1.4024414E-02 assigned positive charge : 456.5319 centred at (gu) : 86.64131 88.26419 86.96493 assigned negative charge : -456.5190 centred at (gu) : 86.64033 87.93549 86.59740 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29459 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 17487 mr = 40097 m= 1533 mr = 11269 m= 37 mr = 643 m= 0 mr = 2 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.3000000 number of dielectric boundary points 29100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 352 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 22038 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) : 0.5315496 object centre at (A) : 14.78900 -4.131500 -16.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7255019E-02 3.4629663E-03 midg,1,midg; midg,igrid,midg -3.0316156E-03 4.7204504E-03 1,midg,midg; igrid,midg,midg -3.1250366E-04 1.2914535E-03 gauss-seidel spectral radius is 0.9981021 estimated iterations to convergence 182 setup time was (sec) 0.5300000 now iterating at: 14:42:20 rms-change max change #iterations 3.178878 138.2466 at 10iterations 1.290997 50.69802 at 20iterations 0.5271246 23.70245 at 30iterations 0.2149518 8.055086 at 40iterations 8.7567724E-02 3.289581 at 50iterations 3.5813391E-02 1.378609 at 60iterations 1.4569672E-02 0.5668278 at 70iterations 5.9426366E-03 0.2465267 at 80iterations 2.4329280E-03 0.1001434 at 90iterations 9.9223643E-04 3.6224365E-02 at 100iterations 4.0588845E-04 1.4818668E-02 at 110iterations 1.6609387E-04 6.1416626E-03 at 120iterations finished qdiffx linear iterations at : 14:42:34 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 1.6609387E-04 6.1416626E-03 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 14:42:35 8.346u 0.251s 0:15.87 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 14:42:35 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIT 148 has a net charge of 0.5140 !!! WARNING: PRO 352 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.391973 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): -18.69800 48.27600 ymin,ymax (A): -28.00600 19.74300 zmin,zma (A): -42.08000 8.813000 x,y,z range (A): 66.97400 47.74900 50.89300 scale (grids/A): 2.391973 object centre (A): 14.78900 -4.131500 -16.63350 number of atom coordinates read : 3036 total number of charged atoms : 2895 net assigned charge : 1.4024414E-02 assigned positive charge : 456.5319 centred at (gu) : 84.96172 87.39616 85.44713 assigned negative charge : -456.5190 centred at (gu) : 84.96046 86.90310 84.89596 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 143960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29459 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 62018 mr = 98686 m= 15953 mr = 47123 m= 2169 mr = 11407 m= 107 mr = 1244 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1443 time to turn everything in is 0.7500000 number of dielectric boundary points 65714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 23112 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) : 1.594649 object centre at (A) : 14.78900 -4.131500 -16.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2796899 6.1918743E-02 midg,1,midg; midg,igrid,midg -3.4717668E-02 6.2170245E-02 1,midg,midg; igrid,midg,midg -0.2332753 0.1426607 gauss-seidel spectral radius is 0.9991147 estimated iterations to convergence 266 setup time was (sec) 0.9800000 now iterating at: 14:42:36 rms-change max change #iterations 8.476909 279.4178 at 10iterations 4.707984 124.4704 at 20iterations 2.596048 64.79155 at 30iterations 1.430465 33.40482 at 40iterations 0.7856231 18.70037 at 50iterations 0.4291247 10.24422 at 60iterations 0.2344619 5.065298 at 70iterations 0.1277942 3.069410 at 80iterations 6.9775969E-02 1.539930 at 90iterations 3.8018025E-02 0.7932014 at 100iterations 2.0670326E-02 0.4512348 at 110iterations 1.1300507E-02 0.2548367 at 120iterations 6.1297971E-03 0.1348991 at 130iterations 3.3406962E-03 8.1405640E-02 at 140iterations 1.8183506E-03 3.8337708E-02 at 150iterations 9.8943815E-04 2.3597717E-02 at 160iterations 5.3953938E-04 1.1833191E-02 at 170iterations 2.9298398E-04 6.6105425E-03 at 180iterations finished qdiffx linear iterations at : 14:43:00 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 2.9298398E-04 6.6105425E-03 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 14:43:01 13.006u 0.221s 0:26.42 50.0% 0+0k 0+0io 0pf+0w