Sat Oct 8 18:26:58 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 8 2011 at 18:26:58 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3240 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: 0.5873037 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): 50.24400 110.8600 ymin,ymax (A): -18.46200 41.14500 zmin,zma (A): -34.63300 24.28800 x,y,z range (A): 60.61600 59.60700 58.92101 scale (grids/A): 0.5873037 object centre (A): 80.55200 11.34150 -5.172502 number of atom coordinates read : 3240 total number of charged atoms : 3098 net assigned charge : 3.500025 assigned positive charge : 483.1587 centred at (gu) : 88.30576 89.47329 91.53856 assigned negative charge : -479.6599 centred at (gu) : 88.25241 89.63526 91.53302 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7561 nv = 96 ne = 84 npr = 64840 no. pairs analyzed = 64840 no. exposed pairs = 4299 no. arc points = 30257 no. surface atoms = 1436 nbur = 1804 mkacc time = 0.1100000 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= 405 mr = 3897 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3064 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9478 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8066685E-10 1.6273826E-09 midg,1,midg; midg,igrid,midg 6.4995347E-09 -3.5017422E-09 1,midg,midg; igrid,midg,midg -9.7213826E-10 1.7439206E-09 gauss-seidel spectral radius is 0.9850642 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 18:26:59 rms-change max change #iterations 0.1116382 17.59088 at 10iterations 9.4631435E-03 1.208944 at 20iterations 1.1433993E-03 0.1820164 at 30iterations 2.6927740E-04 4.1610718E-02 at 40iterations 7.8444602E-05 1.2191772E-02 at 50iterations finished qdiffx linear iterations at : 18:27:01 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 7.8444602E-05 1.2191772E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 18:27:02 3.432u 0.174s 0:04.09 88.0% 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 Sat Oct 8 2011 at 18:27:02 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3240 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: 1.761911 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): 50.24400 110.8600 ymin,ymax (A): -18.46200 41.14500 zmin,zma (A): -34.63300 24.28800 x,y,z range (A): 60.61600 59.60700 58.92101 scale (grids/A): 1.761911 object centre (A): 80.55200 11.34150 -5.172502 number of atom coordinates read : 3240 total number of charged atoms : 3098 net assigned charge : 3.500025 assigned positive charge : 483.1587 centred at (gu) : 84.91637 88.41891 94.61486 assigned negative charge : -479.6599 centred at (gu) : 84.75678 88.90535 94.59864 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82775 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30257 grid for indexing accessible points = 1.400000 m= 28344 mr = 56005 m= 3943 mr = 19749 m= 149 mr = 2101 m= 0 mr = 24 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.4100000 number of dielectric boundary points 37332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 24112 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) : 0.5873037 object centre at (A) : 80.55200 11.34150 -5.172502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9785008E-03 1.8807786E-02 midg,1,midg; midg,igrid,midg 1.7046722E-02 -2.3727765E-02 1,midg,midg; igrid,midg,midg 4.7731567E-03 5.9280344E-03 gauss-seidel spectral radius is 0.9984799 estimated iterations to convergence 203 setup time was (sec) 0.6300000 now iterating at: 18:27:03 rms-change max change #iterations 4.123713 183.4128 at 10iterations 1.840146 63.05544 at 20iterations 0.8230373 27.68114 at 30iterations 0.3702347 11.24442 at 40iterations 0.1665713 5.369916 at 50iterations 7.4583031E-02 2.714369 at 60iterations 3.3599027E-02 1.082001 at 70iterations 1.5120210E-02 0.4745255 at 80iterations 6.8879682E-03 0.2145462 at 90iterations 3.1534536E-03 0.1133366 at 100iterations 1.4741548E-03 4.7065735E-02 at 110iterations 7.1124459E-04 2.4501801E-02 at 120iterations finished qdiffx linear iterations at : 18:27:10 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 7.1124459E-04 2.4501801E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 18:27:11 7.993u 0.187s 0:08.45 96.6% 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 8 2011 at 18:27:11 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3240 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: 2.642867 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): 50.24400 110.8600 ymin,ymax (A): -18.46200 41.14500 zmin,zma (A): -34.63300 24.28800 x,y,z range (A): 60.61600 59.60700 58.92101 scale (grids/A): 2.642867 object centre (A): 80.55200 11.34150 -5.172502 number of atom coordinates read : 3240 total number of charged atoms : 3098 net assigned charge : 3.500025 assigned positive charge : 483.1587 centred at (gu) : 82.37412 87.62812 96.92225 assigned negative charge : -479.6599 centred at (gu) : 82.13513 88.35789 96.89786 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 192034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30257 grid for indexing accessible points = 1.400000 m= 92743 mr = 136709 m= 31391 mr = 73544 m= 6480 mr = 24092 m= 641 mr = 4513 m= 26 mr = 347 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 161 time to turn everything in is 1.030000 number of dielectric boundary points 84109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 24780 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) : 1.761911 object centre at (A) : 80.55200 11.34150 -5.172502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1102152 0.1338587 midg,1,midg; midg,igrid,midg 0.2384322 -0.3144686 1,midg,midg; igrid,midg,midg 0.4436393 2.4944446E-03 gauss-seidel spectral radius is 0.9992350 estimated iterations to convergence 285 setup time was (sec) 1.280000 now iterating at: 18:27:12 rms-change max change #iterations 10.32776 362.9814 at 10iterations 6.108011 186.9315 at 20iterations 3.571841 73.15404 at 30iterations 2.076235 44.00695 at 40iterations 1.202387 25.46817 at 50iterations 0.6955271 14.28199 at 60iterations 0.4004388 7.583267 at 70iterations 0.2300487 4.640431 at 80iterations 0.1318413 2.863701 at 90iterations 7.5535744E-02 1.368804 at 100iterations 4.3238036E-02 0.8367500 at 110iterations 2.4752589E-02 0.4774170 at 120iterations 1.4143372E-02 0.2631912 at 130iterations 8.0716601E-03 0.1396790 at 140iterations 4.6243584E-03 8.9874268E-02 at 150iterations 2.6394380E-03 5.1303864E-02 at 160iterations 1.5162918E-03 2.7496338E-02 at 170iterations 8.7033102E-04 1.5800476E-02 at 180iterations finished qdiffx linear iterations at : 18:27:24 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 8.7033102E-04 1.5800476E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 18:27:24 13.159u 0.190s 0:13.61 98.0% 0+0k 0+0io 0pf+0w