Mon Oct 10 13:56:20 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 Mon Oct 10 2011 at 13:56:20 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3353 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.5786077 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): -24.01600 37.51100 ymin,ymax (A): 20.89700 80.08500 zmin,zma (A): -29.90500 29.36100 x,y,z range (A): 61.52700 59.18800 59.26600 scale (grids/A): 0.5786077 object centre (A): 6.747501 50.49100 -0.2719994 number of atom coordinates read : 3353 total number of charged atoms : 3208 net assigned charge : 12.51404 assigned positive charge : 498.1045 centred at (gu) : 91.73868 89.35621 88.54173 assigned negative charge : -485.5922 centred at (gu) : 91.79586 89.19484 88.48145 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7620 nv = 96 ne = 84 npr = 64865 no. pairs analyzed = 64865 no. exposed pairs = 4549 no. arc points = 32896 no. surface atoms = 1510 nbur = 1843 mkacc time = 0.1800000 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 = 1.484000 m= 373 mr = 3760 m= 3 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3271 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7596227E-09 2.8851974E-09 midg,1,midg; midg,igrid,midg -1.2880209E-09 5.4011875E-09 1,midg,midg; igrid,midg,midg 2.6612785E-09 1.9796011E-09 gauss-seidel spectral radius is 0.9846292 estimated iterations to convergence 66 setup time was (sec) 0.7100000 now iterating at: 13:56:21 rms-change max change #iterations 0.1033538 17.63538 at 10iterations 7.9882275E-03 1.126551 at 20iterations 6.3284906E-04 9.4738007E-02 at 30iterations 5.5401095E-05 7.5912476E-03 at 40iterations 6.6624466E-06 9.7942352E-04 at 50iterations finished qdiffx linear iterations at : 13:56:24 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 6.6624466E-06 9.7942352E-04 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 13:56:25 4.552u 0.253s 0:05.27 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 Mon Oct 10 2011 at 13:56:25 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3353 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.735823 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): -24.01600 37.51100 ymin,ymax (A): 20.89700 80.08500 zmin,zma (A): -29.90500 29.36100 x,y,z range (A): 61.52700 59.18800 59.26600 scale (grids/A): 1.735823 object centre (A): 6.747501 50.49100 -0.2719994 number of atom coordinates read : 3353 total number of charged atoms : 3208 net assigned charge : 12.51404 assigned positive charge : 498.1045 centred at (gu) : 95.21560 88.06805 85.62418 assigned negative charge : -485.5922 centred at (gu) : 95.38719 87.58454 85.44402 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 82788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32896 grid for indexing accessible points = 1.400000 m= 28191 mr = 54391 m= 3839 mr = 19671 m= 146 mr = 2080 m= 0 mr = 17 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 38805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 24951 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) : 0.5786077 object centre at (A) : 6.747501 50.49100 -0.2719994 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0290015E-02 4.0527731E-02 midg,1,midg; midg,igrid,midg -1.4694430E-02 1.5263009E-02 1,midg,midg; igrid,midg,midg 1.4605020E-02 1.2037102E-02 gauss-seidel spectral radius is 0.9984531 estimated iterations to convergence 202 setup time was (sec) 1.090000 now iterating at: 13:56:26 rms-change max change #iterations 4.015464 149.1649 at 10iterations 1.773106 74.85088 at 20iterations 0.7881116 24.87896 at 30iterations 0.3497157 10.55025 at 40iterations 0.1559088 4.547932 at 50iterations 6.9438666E-02 2.170924 at 60iterations 3.0830828E-02 0.9135189 at 70iterations 1.3727019E-02 0.4547606 at 80iterations 6.1226673E-03 0.1957083 at 90iterations 2.7317305E-03 8.6920738E-02 at 100iterations 1.2176122E-03 4.1484833E-02 at 110iterations 5.4186175E-04 1.9905090E-02 at 120iterations finished qdiffx linear iterations at : 13:56:35 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 5.4186175E-04 1.9905090E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 13:56:36 9.792u 0.259s 0:10.54 95.2% 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 13:56:36 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3353 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.603735 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): -24.01600 37.51100 ymin,ymax (A): 20.89700 80.08500 zmin,zma (A): -29.90500 29.36100 x,y,z range (A): 61.52700 59.18800 59.26600 scale (grids/A): 2.603735 object centre (A): 6.747501 50.49100 -0.2719994 number of atom coordinates read : 3353 total number of charged atoms : 3208 net assigned charge : 12.51404 assigned positive charge : 498.1045 centred at (gu) : 97.82303 87.10181 83.43603 assigned negative charge : -485.5922 centred at (gu) : 98.08057 86.37667 83.16592 start vw surface at 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 191402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32896 grid for indexing accessible points = 1.400000 m= 92661 mr = 133050 m= 31514 mr = 73085 m= 6661 mr = 24316 m= 597 mr = 4561 m= 9 mr = 275 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.610000 number of dielectric boundary points 87557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 25663 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) : 1.735823 object centre at (A) : 6.747501 50.49100 -0.2719994 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4163764 0.5927877 midg,1,midg; midg,igrid,midg -0.1185918 0.1887093 1,midg,midg; igrid,midg,midg 8.1657030E-02 0.1340826 gauss-seidel spectral radius is 0.9992339 estimated iterations to convergence 285 setup time was (sec) 1.970000 now iterating at: 13:56:38 rms-change max change #iterations 10.06172 290.5169 at 10iterations 5.892415 125.5857 at 20iterations 3.410180 70.11037 at 30iterations 1.972722 40.84385 at 40iterations 1.136154 24.69020 at 50iterations 0.6523532 12.30368 at 60iterations 0.3732019 6.906574 at 70iterations 0.2135458 4.074533 at 80iterations 0.1220401 2.333565 at 90iterations 6.9774389E-02 1.246028 at 100iterations 3.9682675E-02 0.8239069 at 110iterations 2.2679716E-02 0.4291077 at 120iterations 1.2930313E-02 0.2323055 at 130iterations 7.3562325E-03 0.1387892 at 140iterations 4.1935267E-03 8.0410004E-02 at 150iterations 2.3920196E-03 4.0919304E-02 at 160iterations 1.3618934E-03 2.5222778E-02 at 170iterations 7.7714905E-04 1.3465881E-02 at 180iterations finished qdiffx linear iterations at : 13:56:51 total time elapsed so far: 15.61000 # loops : 180 mean,max change (kT/e) : 7.7714905E-04 1.3465881E-02 energy calculations done at 15.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.80000 DelPhi exited at 13:56:52 15.797u 0.286s 0:16.40 97.9% 0+0k 0+0io 0pf+0w