Mon Oct 10 16:59:12 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+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 Mon Oct 10 2011 at 16:59:12 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2609 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: 0.5699465 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): 9.882999 63.96100 ymin,ymax (A): -27.01400 18.50100 zmin,zma (A): 0.9179999 63.38000 x,y,z range (A): 54.07800 45.51500 62.46200 scale (grids/A): 0.5699465 object centre (A): 36.92200 -4.256500 32.14900 number of atom coordinates read : 2609 total number of charged atoms : 2453 net assigned charge : 9.500017 assigned positive charge : 383.0797 centred at (gu) : 91.82199 90.32076 90.34364 assigned negative charge : -373.5808 centred at (gu) : 91.86055 90.14903 90.32375 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5804 nv = 96 ne = 84 npr = 49970 no. pairs analyzed = 49970 no. exposed pairs = 3545 no. arc points = 26124 no. surface atoms = 1193 nbur = 1416 mkacc time = 8.9999996E-02 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 = 1.512000 m= 251 mr = 2837 m= 0 mr = 14 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2589 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7231 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1008889E-09 1.8554941E-09 midg,1,midg; midg,igrid,midg -7.8129930E-10 3.9509507E-09 1,midg,midg; igrid,midg,midg 1.2842177E-09 1.4254357E-09 gauss-seidel spectral radius is 0.9840969 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 16:59:13 rms-change max change #iterations 8.1332408E-02 20.43341 at 10iterations 6.0426742E-03 0.9169159 at 20iterations 4.5580973E-04 7.7232361E-02 at 30iterations 3.7097925E-05 6.7291260E-03 at 40iterations 3.4174852E-06 4.8637390E-04 at 50iterations finished qdiffx linear iterations at : 16:59:15 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.4174852E-06 4.8637390E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 16:59:16 3.396u 0.176s 0:04.02 88.5% 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 Mon Oct 10 2011 at 16:59:16 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2609 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: 1.709840 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): 9.882999 63.96100 ymin,ymax (A): -27.01400 18.50100 zmin,zma (A): 0.9179999 63.38000 x,y,z range (A): 54.07800 45.51500 62.46200 scale (grids/A): 1.709840 object centre (A): 36.92200 -4.256500 32.14900 number of atom coordinates read : 2609 total number of charged atoms : 2453 net assigned charge : 9.500017 assigned positive charge : 383.0797 centred at (gu) : 95.46523 90.96191 91.03032 assigned negative charge : -373.5808 centred at (gu) : 95.58143 90.44720 90.97115 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26124 grid for indexing accessible points = 1.400000 m= 19815 mr = 41163 m= 2242 mr = 13433 m= 71 mr = 1034 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 356 time to turn everything in is 0.3200000 number of dielectric boundary points 29521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 18946 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) : 0.5699465 object centre at (A) : 36.92200 -4.256500 32.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4361671E-02 2.7443066E-02 midg,1,midg; midg,igrid,midg -6.2335483E-03 1.6884461E-02 1,midg,midg; igrid,midg,midg 1.1387499E-02 5.4117097E-03 gauss-seidel spectral radius is 0.9983254 estimated iterations to convergence 194 setup time was (sec) 0.5200000 now iterating at: 16:59:17 rms-change max change #iterations 3.342561 153.5869 at 10iterations 1.428442 59.60831 at 20iterations 0.6135308 23.84393 at 30iterations 0.2646045 12.58567 at 40iterations 0.1139525 4.556839 at 50iterations 4.9235478E-02 1.851246 at 60iterations 2.1138312E-02 0.7242298 at 70iterations 9.1476338E-03 0.3534412 at 80iterations 3.9405017E-03 0.1478364 at 90iterations 1.7031656E-03 6.0990810E-02 at 100iterations 7.3665538E-04 2.5802612E-02 at 110iterations 3.1632103E-04 1.2167454E-02 at 120iterations finished qdiffx linear iterations at : 16:59:24 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 3.1632103E-04 1.2167454E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 16:59:24 7.797u 0.217s 0:08.38 95.4% 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 Mon Oct 10 2011 at 16:59:24 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2609 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: 2.564759 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): 9.882999 63.96100 ymin,ymax (A): -27.01400 18.50100 zmin,zma (A): 0.9179999 63.38000 x,y,z range (A): 54.07800 45.51500 62.46200 scale (grids/A): 2.564759 object centre (A): 36.92200 -4.256500 32.14900 number of atom coordinates read : 2609 total number of charged atoms : 2453 net assigned charge : 9.500017 assigned positive charge : 383.0797 centred at (gu) : 98.19764 91.44274 91.54536 assigned negative charge : -373.5808 centred at (gu) : 98.37223 90.67073 91.45674 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 146079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26124 grid for indexing accessible points = 1.400000 m= 67381 mr = 100953 m= 20227 mr = 52395 m= 3573 mr = 15015 m= 295 mr = 2269 m= 11 mr = 146 m= 0 mr = 4 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1157 time to turn everything in is 0.7500000 number of dielectric boundary points 66784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 19613 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) : 1.709840 object centre at (A) : 36.92200 -4.256500 32.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2257424 0.5053039 midg,1,midg; midg,igrid,midg -6.6591382E-02 0.2234364 1,midg,midg; igrid,midg,midg 0.1645002 4.8989128E-02 gauss-seidel spectral radius is 0.9991827 estimated iterations to convergence 276 setup time was (sec) 0.9900000 now iterating at: 16:59:26 rms-change max change #iterations 8.523872 357.9615 at 10iterations 4.876412 118.8711 at 20iterations 2.774105 78.40302 at 30iterations 1.572389 41.65660 at 40iterations 0.8895138 21.13415 at 50iterations 0.5002766 11.86085 at 60iterations 0.2805472 7.044518 at 70iterations 0.1570135 3.565349 at 80iterations 8.8011645E-02 1.890598 at 90iterations 4.9355756E-02 1.157688 at 100iterations 2.7583174E-02 0.6382637 at 110iterations 1.5423779E-02 0.3571444 at 120iterations 8.5959807E-03 0.1814036 at 130iterations 4.8126634E-03 9.8344803E-02 at 140iterations 2.6836582E-03 5.7470798E-02 at 150iterations 1.4955887E-03 3.2940865E-02 at 160iterations 8.3584932E-04 1.6320705E-02 at 170iterations 4.6618044E-04 9.6359253E-03 at 180iterations finished qdiffx linear iterations at : 16:59:37 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 4.6618044E-04 9.6359253E-03 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 16:59:38 12.366u 0.213s 0:13.83 90.8% 0+0k 0+0io 0pf+0w