Sat Oct 8 20:41:56 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 20:41:56 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 454 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6158423 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): -31.11700 17.15800 ymin,ymax (A): -23.72100 23.46300 zmin,zma (A): -12.57400 45.23300 x,y,z range (A): 48.27500 47.18400 57.80700 scale (grids/A): 0.6158423 object centre (A): -6.979500 -0.1289997 16.32950 number of atom coordinates read : 2588 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.2440 centred at (gu) : 88.55452 89.10659 89.67251 assigned negative charge : -388.3386 centred at (gu) : 88.46261 89.15079 89.53812 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6296 nv = 96 ne = 84 npr = 54238 no. pairs analyzed = 54238 no. exposed pairs = 3029 no. arc points = 21406 no. surface atoms = 1022 nbur = 1566 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 314 mr = 3478 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.3200000 number of dielectric boundary points 3109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2126 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7929 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5603966E-09 9.8830597E-09 midg,1,midg; midg,igrid,midg 6.6286110E-09 2.2892409E-10 1,midg,midg; igrid,midg,midg -3.6738532E-09 5.9660006E-09 gauss-seidel spectral radius is 0.9863411 estimated iterations to convergence 70 setup time was (sec) 0.5600000 now iterating at: 20:41:57 rms-change max change #iterations 0.1221815 20.35833 at 10iterations 1.1214298E-02 1.678719 at 20iterations 1.0477959E-03 0.1705093 at 30iterations 1.0875012E-04 1.8877029E-02 at 40iterations 1.4455084E-05 3.2005310E-03 at 50iterations finished qdiffx linear iterations at : 20:41:59 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.4455084E-05 3.2005310E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 20:42:00 3.338u 0.189s 0:03.82 91.8% 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 20:42:00 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 454 has a net charge of 1.4000 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: 1.847527 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): -31.11700 17.15800 ymin,ymax (A): -23.72100 23.46300 zmin,zma (A): -12.57400 45.23300 x,y,z range (A): 48.27500 47.18400 57.80700 scale (grids/A): 1.847527 object centre (A): -6.979500 -0.1289997 16.32950 number of atom coordinates read : 2588 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.2440 centred at (gu) : 85.66321 87.31947 89.01668 assigned negative charge : -388.3386 centred at (gu) : 85.38777 87.45215 88.61423 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21406 grid for indexing accessible points = 1.400000 m= 23639 mr = 48578 m= 3250 mr = 17273 m= 121 mr = 1903 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3244 time to turn everything in is 0.5200000 number of dielectric boundary points 28614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19241 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) : 0.6158423 object centre at (A) : -6.979500 -0.1289997 16.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9289445E-02 2.8698910E-02 midg,1,midg; midg,igrid,midg 1.0789837E-02 -1.3843623E-04 1,midg,midg; igrid,midg,midg -1.6811725E-03 3.1880956E-02 gauss-seidel spectral radius is 0.9985458 estimated iterations to convergence 208 setup time was (sec) 0.8100000 now iterating at: 20:42:01 rms-change max change #iterations 3.949387 171.9999 at 10iterations 1.813781 61.70288 at 20iterations 0.8240185 31.19980 at 30iterations 0.3766996 15.77872 at 40iterations 0.1728153 5.692856 at 50iterations 7.8951329E-02 2.518785 at 60iterations 3.6062174E-02 1.189005 at 70iterations 1.6470496E-02 0.5082664 at 80iterations 7.5349240E-03 0.2652473 at 90iterations 3.4512710E-03 0.1184311 at 100iterations 1.5834729E-03 4.9449921E-02 at 110iterations 7.2371919E-04 2.5428772E-02 at 120iterations finished qdiffx linear iterations at : 20:42:07 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 7.2371919E-04 2.5428772E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 20:42:08 7.489u 0.221s 0:08.00 96.2% 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 Sat Oct 8 2011 at 20:42:08 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 454 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.771291 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): -31.11700 17.15800 ymin,ymax (A): -23.72100 23.46300 zmin,zma (A): -12.57400 45.23300 x,y,z range (A): 48.27500 47.18400 57.80700 scale (grids/A): 2.771291 object centre (A): -6.979500 -0.1289997 16.32950 number of atom coordinates read : 2588 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.2440 centred at (gu) : 83.49454 85.97908 88.52490 assigned negative charge : -388.3386 centred at (gu) : 83.08154 86.17824 87.92115 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 161000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21406 grid for indexing accessible points = 1.400000 m= 78478 mr = 117815 m= 26052 mr = 64221 m= 5479 mr = 20715 m= 517 mr = 3941 m= 14 mr = 286 m= 0 mr = 2 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 10994 time to turn everything in is 1.250000 number of dielectric boundary points 64560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 19599 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) : 1.847527 object centre at (A) : -6.979500 -0.1289997 16.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1162395 0.3345283 midg,1,midg; midg,igrid,midg 0.1287014 -1.6753882E-02 1,midg,midg; igrid,midg,midg -1.0055832E-02 0.4087791 gauss-seidel spectral radius is 0.9992285 estimated iterations to convergence 284 setup time was (sec) 1.570000 now iterating at: 20:42:10 rms-change max change #iterations 9.378004 325.1259 at 10iterations 5.388919 124.5596 at 20iterations 3.075637 65.75765 at 30iterations 1.755422 39.82774 at 40iterations 0.9989425 20.26002 at 50iterations 0.5683048 11.21368 at 60iterations 0.3235153 5.904463 at 70iterations 0.1834181 3.593370 at 80iterations 0.1044102 1.966936 at 90iterations 5.9227165E-02 1.116815 at 100iterations 3.3599474E-02 0.7217741 at 110iterations 1.9065665E-02 0.3539047 at 120iterations 1.0832373E-02 0.2147484 at 130iterations 6.1492901E-03 0.1128197 at 140iterations 3.4912003E-03 6.6695213E-02 at 150iterations 1.9830267E-03 3.9447546E-02 at 160iterations 1.1270690E-03 2.3359299E-02 at 170iterations 6.3914777E-04 1.1310577E-02 at 180iterations finished qdiffx linear iterations at : 20:42:20 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 6.3914777E-04 1.1310577E-02 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 20:42:21 12.124u 0.218s 0:12.60 97.8% 0+0k 0+0io 0pf+0w