Tue Oct 11 07:26:08 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 Tue Oct 11 2011 at 07:26:08 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4806 !!! WARNING: UMP 1582 has a net charge of -0.1000 !!! WARNING: UMP 1587 has a net charge of -0.1000 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: 0.4647398 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): -27.32200 49.28000 ymin,ymax (A): -0.8800000 55.18700 zmin,zma (A): -42.52300 22.84300 x,y,z range (A): 76.60200 56.06700 65.36600 scale (grids/A): 0.4647398 object centre (A): 10.97900 27.15350 -9.840001 number of atom coordinates read : 4806 total number of charged atoms : 4628 net assigned charge : -3.199986 assigned positive charge : 725.9523 centred at (gu) : 90.18122 90.26353 90.58950 assigned negative charge : -729.1566 centred at (gu) : 90.11821 90.24734 90.63113 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6315 nv = 96 ne = 84 npr = 97110 no. pairs analyzed = 97110 no. exposed pairs = 6131 no. arc points = 41588 no. surface atoms = 2074 nbur = 2732 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 = 1.820000 m= 181 mr = 3181 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3754 ## 713 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 8684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6623517E-12 -2.0955401E-11 midg,1,midg; midg,igrid,midg -9.0666667E-12 2.1434250E-13 1,midg,midg; igrid,midg,midg -2.3100206E-11 1.5213202E-11 gauss-seidel spectral radius is 0.9763557 estimated iterations to convergence 54 setup time was (sec) 0.7000000 now iterating at: 07:26:09 rms-change max change #iterations 4.0583536E-02 8.874619 at 10iterations 3.1709946E-03 0.4445019 at 20iterations 9.4641326E-04 0.1215248 at 30iterations 3.4131453E-04 4.1840553E-02 at 40iterations 1.2570698E-04 1.5980721E-02 at 50iterations finished qdiffx linear iterations at : 07:26:12 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.2570698E-04 1.5980721E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 07:26:13 3.497u 0.175s 0:04.28 85.5% 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 Tue Oct 11 2011 at 07:26:13 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4806 !!! WARNING: UMP 1582 has a net charge of -0.1000 !!! WARNING: UMP 1587 has a net charge of -0.1000 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: 1.394220 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): -27.32200 49.28000 ymin,ymax (A): -0.8800000 55.18700 zmin,zma (A): -42.52300 22.84300 x,y,z range (A): 76.60200 56.06700 65.36600 scale (grids/A): 1.394220 object centre (A): 10.97900 27.15350 -9.840001 number of atom coordinates read : 4806 total number of charged atoms : 4628 net assigned charge : -3.199986 assigned positive charge : 725.9523 centred at (gu) : 90.54236 90.78918 91.76714 assigned negative charge : -729.1566 centred at (gu) : 90.35446 90.74178 91.89307 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41588 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 18585 mr = 49287 m= 1117 mr = 11907 m= 8 mr = 358 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1320 time to turn everything in is 0.5400000 number of dielectric boundary points 31162 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 660 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 33449 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) : 0.4647398 object centre at (A) : 10.97900 27.15350 -9.840001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0429641E-03 -7.8927958E-03 midg,1,midg; midg,igrid,midg -3.2660207E-03 -9.0021954E-04 1,midg,midg; igrid,midg,midg -8.3831977E-03 1.0640876E-02 gauss-seidel spectral radius is 0.9976535 estimated iterations to convergence 164 setup time was (sec) 0.8200000 now iterating at: 07:26:14 rms-change max change #iterations 3.033570 128.5462 at 10iterations 1.123520 45.72450 at 20iterations 0.4166787 17.06169 at 30iterations 0.1546335 6.297666 at 40iterations 5.7638805E-02 2.130508 at 50iterations 2.1705430E-02 0.8028002 at 60iterations 8.4512606E-03 0.3099098 at 70iterations 3.5917487E-03 0.1260319 at 80iterations 1.7829736E-03 7.0517540E-02 at 90iterations 1.0544497E-03 3.2975435E-02 at 100iterations 6.9213187E-04 2.0383835E-02 at 110iterations 4.7426988E-04 1.2777328E-02 at 120iterations finished qdiffx linear iterations at : 07:26:20 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 4.7426988E-04 1.2777328E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 07:26:22 7.507u 0.222s 0:08.92 86.5% 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 Tue Oct 11 2011 at 07:26:22 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4806 !!! WARNING: UMP 1582 has a net charge of -0.1000 !!! WARNING: UMP 1587 has a net charge of -0.1000 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: 2.091329 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): -27.32200 49.28000 ymin,ymax (A): -0.8800000 55.18700 zmin,zma (A): -42.52300 22.84300 x,y,z range (A): 76.60200 56.06700 65.36600 scale (grids/A): 2.091329 object centre (A): 10.97900 27.15350 -9.840001 number of atom coordinates read : 4806 total number of charged atoms : 4628 net assigned charge : -3.199986 assigned positive charge : 725.9523 centred at (gu) : 90.81300 91.18346 92.65005 assigned negative charge : -729.1566 centred at (gu) : 90.53165 91.11260 92.83955 start vw surface at 0.2100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 170614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41588 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 70013 mr = 121535 m= 14367 mr = 53820 m= 1304 mr = 9993 m= 28 mr = 641 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 4542 time to turn everything in is 1.230000 number of dielectric boundary points 70337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 36772 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) : 1.394220 object centre at (A) : 10.97900 27.15350 -9.840001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5956083E-02 -0.2271252 midg,1,midg; midg,igrid,midg -7.5523406E-02 -2.1092655E-02 1,midg,midg; igrid,midg,midg -0.2976684 0.2431961 gauss-seidel spectral radius is 0.9990091 estimated iterations to convergence 251 setup time was (sec) 1.540000 now iterating at: 07:26:24 rms-change max change #iterations 8.806006 266.8446 at 10iterations 4.785482 134.1550 at 20iterations 2.586103 90.86200 at 30iterations 1.388774 38.01489 at 40iterations 0.7421681 17.70561 at 50iterations 0.3972339 9.037531 at 60iterations 0.2107853 4.562406 at 70iterations 0.1120713 2.506462 at 80iterations 5.9330184E-02 1.405081 at 90iterations 3.1533692E-02 0.6839275 at 100iterations 1.6657494E-02 0.3892355 at 110iterations 8.8274274E-03 0.1791077 at 120iterations 4.6870238E-03 0.1091337 at 130iterations 2.4874841E-03 5.3146362E-02 at 140iterations 1.3287927E-03 2.7130127E-02 at 150iterations 7.1731501E-04 1.5792847E-02 at 160iterations 3.9765393E-04 8.4037781E-03 at 170iterations 2.2985903E-04 5.2995682E-03 at 180iterations finished qdiffx linear iterations at : 07:26:34 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 2.2985903E-04 5.2995682E-03 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 07:26:35 12.106u 0.221s 0:12.97 94.9% 0+0k 0+0io 0pf+0w