Sun Oct 9 00:34:52 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+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 Sun Oct 9 2011 at 00:34:52 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 = 2872 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5827277 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): 48.03900 94.30700 ymin,ymax (A): 22.71400 83.80600 zmin,zma (A): -14.27100 41.56600 x,y,z range (A): 46.26800 61.09200 55.83700 scale (grids/A): 0.5827277 object centre (A): 71.17300 53.26000 13.64750 number of atom coordinates read : 2872 total number of charged atoms : 2729 net assigned charge : 4.226037 assigned positive charge : 420.5255 centred at (gu) : 90.89693 89.27587 88.06110 assigned negative charge : -416.3006 centred at (gu) : 90.79866 89.12453 87.95313 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6642 nv = 96 ne = 84 npr = 57614 no. pairs analyzed = 57614 no. exposed pairs = 3631 no. arc points = 25887 no. surface atoms = 1211 nbur = 1661 mkacc time = 0.1200000 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 = 1.456000 m= 285 mr = 3561 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3300000 number of dielectric boundary points 3352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2553 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8267 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2351234E-09 2.2114233E-09 midg,1,midg; midg,igrid,midg -2.8411336E-09 3.7193695E-09 1,midg,midg; igrid,midg,midg -9.2646368E-10 4.0118975E-09 gauss-seidel spectral radius is 0.9847954 estimated iterations to convergence 67 setup time was (sec) 0.5500000 now iterating at: 00:34:53 rms-change max change #iterations 9.9586554E-02 14.40733 at 10iterations 7.9135252E-03 1.281345 at 20iterations 6.0993468E-04 8.9222908E-02 at 30iterations 4.9441758E-05 8.8176727E-03 at 40iterations 3.8881262E-06 6.1607361E-04 at 50iterations finished qdiffx linear iterations at : 00:34:55 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 3.8881262E-06 6.1607361E-04 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 00:34:56 3.129u 0.123s 0:03.56 91.0% 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 00:34:56 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 = 2872 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.748183 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): 48.03900 94.30700 ymin,ymax (A): 22.71400 83.80600 zmin,zma (A): -14.27100 41.56600 x,y,z range (A): 46.26800 61.09200 55.83700 scale (grids/A): 1.748183 object centre (A): 71.17300 53.26000 13.64750 number of atom coordinates read : 2872 total number of charged atoms : 2729 net assigned charge : 4.226037 assigned positive charge : 420.5255 centred at (gu) : 92.69017 87.82718 84.18264 assigned negative charge : -416.3006 centred at (gu) : 92.39618 87.37331 83.85936 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25887 grid for indexing accessible points = 1.400000 m= 24512 mr = 49887 m= 3175 mr = 17619 m= 101 mr = 1756 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1090 time to turn everything in is 0.5300000 number of dielectric boundary points 31114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 21195 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) : 0.5827277 object centre at (A) : 71.17300 53.26000 13.64750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3893792E-03 2.0164281E-02 midg,1,midg; midg,igrid,midg 7.9108337E-03 2.8694687E-02 1,midg,midg; igrid,midg,midg -8.4495516E-03 4.1299067E-03 gauss-seidel spectral radius is 0.9984137 estimated iterations to convergence 199 setup time was (sec) 0.7900000 now iterating at: 00:34:57 rms-change max change #iterations 3.723549 171.9699 at 10iterations 1.631282 62.65504 at 20iterations 0.7179523 26.89133 at 30iterations 0.3161458 10.84921 at 40iterations 0.1389001 4.254738 at 50iterations 6.1674986E-02 2.021919 at 60iterations 2.7121663E-02 0.9034996 at 70iterations 1.1969890E-02 0.4047165 at 80iterations 5.2840873E-03 0.1771765 at 90iterations 2.3381882E-03 8.2485199E-02 at 100iterations 1.0358799E-03 3.5317123E-02 at 110iterations 4.5529337E-04 1.5308380E-02 at 120iterations finished qdiffx linear iterations at : 00:35:03 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 4.5529337E-04 1.5308380E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 00:35:04 7.022u 0.166s 0:07.53 95.3% 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 00:35:04 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 = 2872 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.622275 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): 48.03900 94.30700 ymin,ymax (A): 22.71400 83.80600 zmin,zma (A): -14.27100 41.56600 x,y,z range (A): 46.26800 61.09200 55.83700 scale (grids/A): 2.622275 object centre (A): 71.17300 53.26000 13.64750 number of atom coordinates read : 2872 total number of charged atoms : 2729 net assigned charge : 4.226037 assigned positive charge : 420.5255 centred at (gu) : 94.03506 86.74070 81.27385 assigned negative charge : -416.3006 centred at (gu) : 93.59422 86.06000 80.78899 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 168055 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25887 grid for indexing accessible points = 1.400000 m= 81557 mr = 121167 m= 26563 mr = 65892 m= 5225 mr = 20727 m= 458 mr = 3652 m= 11 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 3774 time to turn everything in is 1.200000 number of dielectric boundary points 70209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 21817 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) : 1.748183 object centre at (A) : 71.17300 53.26000 13.64750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1387437 0.3772041 midg,1,midg; midg,igrid,midg 0.2171243 0.3884063 1,midg,midg; igrid,midg,midg -7.1656860E-02 5.9931900E-02 gauss-seidel spectral radius is 0.9992038 estimated iterations to convergence 280 setup time was (sec) 1.480000 now iterating at: 00:35:05 rms-change max change #iterations 9.256655 359.9405 at 10iterations 5.330320 163.0722 at 20iterations 3.037072 80.98376 at 30iterations 1.721776 35.89454 at 40iterations 0.9765156 20.19971 at 50iterations 0.5521843 10.94819 at 60iterations 0.3104960 6.177702 at 70iterations 0.1755682 3.234379 at 80iterations 9.8528735E-02 1.784050 at 90iterations 5.5555303E-02 1.038071 at 100iterations 3.1244412E-02 0.5823231 at 110iterations 1.7583681E-02 0.3415699 at 120iterations 9.8874802E-03 0.1834488 at 130iterations 5.5570966E-03 0.1108056 at 140iterations 3.1197986E-03 6.0647964E-02 at 150iterations 1.7595125E-03 3.5324097E-02 at 160iterations 9.8735746E-04 1.7890573E-02 at 170iterations 5.5587012E-04 9.7818375E-03 at 180iterations finished qdiffx linear iterations at : 00:35:15 total time elapsed so far: 10.95000 # loops : 180 mean,max change (kT/e) : 5.5587012E-04 9.7818375E-03 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 00:35:15 11.126u 0.169s 0:11.63 96.9% 0+0k 0+0io 0pf+0w