Mon Oct 10 19:37:49 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 19:37:49 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 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: 0.5440430 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): -9.367001 46.62400 ymin,ymax (A): -43.67800 21.75800 zmin,zma (A): -76.67000 -13.94000 x,y,z range (A): 55.99100 65.43600 62.73000 scale (grids/A): 0.5440430 object centre (A): 18.62850 -10.96000 -45.30500 number of atom coordinates read : 3221 total number of charged atoms : 3078 net assigned charge : -4.999978 assigned positive charge : 476.5057 centred at (gu) : 89.59628 89.87002 92.51509 assigned negative charge : -481.5074 centred at (gu) : 89.63671 90.02972 92.40725 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6496 nv = 96 ne = 84 npr = 61825 no. pairs analyzed = 61825 no. exposed pairs = 5014 no. arc points = 35505 no. surface atoms = 1661 nbur = 1560 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 = 1.596000 m= 273 mr = 2746 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3561 ## 464 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8388 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5746513E-10 7.7652418E-10 midg,1,midg; midg,igrid,midg 7.5694795E-10 -1.3461573E-09 1,midg,midg; igrid,midg,midg -4.3446850E-11 -5.2324417E-10 gauss-seidel spectral radius is 0.9826261 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 19:37:50 rms-change max change #iterations 7.3713347E-02 13.68866 at 10iterations 5.9478944E-03 1.094559 at 20iterations 1.6747129E-03 0.2631989 at 30iterations 7.6467113E-04 0.1343517 at 40iterations 3.6240398E-04 6.7642212E-02 at 50iterations finished qdiffx linear iterations at : 19:37:54 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 3.6240398E-04 6.7642212E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 19:37:55 4.203u 0.277s 0:05.19 86.1% 0+0k 0+0io 6pf+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 19:37:55 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 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: 1.632129 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): -9.367001 46.62400 ymin,ymax (A): -43.67800 21.75800 zmin,zma (A): -76.67000 -13.94000 x,y,z range (A): 55.99100 65.43600 62.73000 scale (grids/A): 1.632129 object centre (A): 18.62850 -10.96000 -45.30500 number of atom coordinates read : 3221 total number of charged atoms : 3078 net assigned charge : -4.999978 assigned positive charge : 476.5057 centred at (gu) : 88.78777 89.60940 97.54449 assigned negative charge : -481.5074 centred at (gu) : 88.90991 90.08910 97.22150 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 70647 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35505 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20499 mr = 42797 m= 2181 mr = 12352 m= 59 mr = 810 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 37426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 23546 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) : 0.5440430 object centre at (A) : 18.62850 -10.96000 -45.30500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3811724E-02 9.1786003E-03 midg,1,midg; midg,igrid,midg 2.6185831E-02 -1.2661068E-02 1,midg,midg; igrid,midg,midg -1.1445839E-02 -1.1654578E-02 gauss-seidel spectral radius is 0.9982383 estimated iterations to convergence 189 setup time was (sec) 0.9600000 now iterating at: 19:37:56 rms-change max change #iterations 3.432150 154.4251 at 10iterations 1.443573 56.34891 at 20iterations 0.6033223 21.98090 at 30iterations 0.2543083 10.26489 at 40iterations 0.1071525 3.872348 at 50iterations 4.5316018E-02 1.723290 at 60iterations 1.9510038E-02 0.7322006 at 70iterations 8.7372232E-03 0.3540268 at 80iterations 4.2977477E-03 0.1735306 at 90iterations 2.4901873E-03 9.0024948E-02 at 100iterations 1.6841235E-03 6.0630798E-02 at 110iterations 1.2282273E-03 4.5511246E-02 at 120iterations finished qdiffx linear iterations at : 19:38:04 total time elapsed so far: 9.500000 # loops : 120 mean,max change (kT/e) : 1.2282273E-03 4.5511246E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 19:38:05 9.674u 0.327s 0:10.43 95.7% 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 19:38:05 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 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: 2.448194 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): -9.367001 46.62400 ymin,ymax (A): -43.67800 21.75800 zmin,zma (A): -76.67000 -13.94000 x,y,z range (A): 55.99100 65.43600 62.73000 scale (grids/A): 2.448194 object centre (A): 18.62850 -10.96000 -45.30500 number of atom coordinates read : 3221 total number of charged atoms : 3078 net assigned charge : -4.999978 assigned positive charge : 476.5057 centred at (gu) : 88.18143 89.41383 101.3165 assigned negative charge : -481.5074 centred at (gu) : 88.36493 90.13371 100.8323 start vw surface at 0.1800000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 163581 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35505 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 70037 mr = 106410 m= 19970 mr = 50765 m= 3059 mr = 13441 m= 171 mr = 1627 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.610000 number of dielectric boundary points 84527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 24601 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) : 1.632129 object centre at (A) : 18.62850 -10.96000 -45.30500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2095149 0.1030115 midg,1,midg; midg,igrid,midg 0.5700514 -0.1324968 1,midg,midg; igrid,midg,midg -0.1067723 -0.1268065 gauss-seidel spectral radius is 0.9991767 estimated iterations to convergence 275 setup time was (sec) 1.940000 now iterating at: 19:38:07 rms-change max change #iterations 9.298018 285.8024 at 10iterations 5.399856 171.9948 at 20iterations 3.106969 76.35173 at 30iterations 1.779034 40.68831 at 40iterations 1.007263 21.61662 at 50iterations 0.5683627 13.28202 at 60iterations 0.3207937 6.580437 at 70iterations 0.1797055 3.884665 at 80iterations 0.1010480 2.282480 at 90iterations 5.6649007E-02 1.272139 at 100iterations 3.1797506E-02 0.6737652 at 110iterations 1.7911490E-02 0.3855667 at 120iterations 1.0155352E-02 0.2246132 at 130iterations 5.8631753E-03 0.1299858 at 140iterations 3.5171376E-03 7.2759628E-02 at 150iterations 2.2359774E-03 4.6668053E-02 at 160iterations 1.5444667E-03 3.3004761E-02 at 170iterations 1.1533079E-03 2.5857925E-02 at 180iterations finished qdiffx linear iterations at : 19:38:22 total time elapsed so far: 16.16000 # loops : 180 mean,max change (kT/e) : 1.1533079E-03 2.5857925E-02 energy calculations done at 16.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.35000 DelPhi exited at 19:38:22 16.355u 0.311s 0:16.96 98.2% 0+0k 0+0io 0pf+0w