Mon Oct 10 12:13:51 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 12:13:51 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7614973 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): 8.905001 54.98900 ymin,ymax (A): -8.872000 35.88500 zmin,zma (A): -3.076000 43.67400 x,y,z range (A): 46.08400 44.75700 46.75000 scale (grids/A): 0.7614973 object centre (A): 31.94700 13.50650 20.29900 number of atom coordinates read : 2117 total number of charged atoms : 1976 net assigned charge : -6.746984 assigned positive charge : 317.4199 centred at (gu) : 89.56281 90.63155 90.18193 assigned negative charge : -324.1670 centred at (gu) : 89.56814 90.72538 90.35593 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8397 nv = 96 ne = 84 npr = 44123 no. pairs analyzed = 44123 no. exposed pairs = 2688 no. arc points = 18901 no. surface atoms = 909 nbur = 1208 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 666 mr = 4687 m= 7 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 158 time to turn everything in is 0.2900000 number of dielectric boundary points 4229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1452 ## 109 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1341419E-08 -4.7937561E-07 midg,1,midg; midg,igrid,midg -3.5541806E-08 -3.7477949E-07 1,midg,midg; igrid,midg,midg -1.9078038E-07 -1.7922392E-07 gauss-seidel spectral radius is 0.9910098 estimated iterations to convergence 86 setup time was (sec) 0.7700000 now iterating at: 12:13:52 rms-change max change #iterations 0.2734313 37.60695 at 10iterations 3.8575348E-02 4.412086 at 20iterations 5.5368780E-03 0.7253928 at 30iterations 7.8847236E-04 9.2358589E-02 at 40iterations 1.1336328E-04 1.3050556E-02 at 50iterations finished qdiffx linear iterations at : 12:14:00 total time elapsed so far: 8.670000 # loops : 50 mean,max change (kT/e) : 1.1336328E-04 1.3050556E-02 energy calculations done at 8.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.860000 DelPhi exited at 12:14:01 8.862u 0.710s 0:09.92 96.4% 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 12:14:01 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.284492 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): 8.905001 54.98900 ymin,ymax (A): -8.872000 35.88500 zmin,zma (A): -3.076000 43.67400 x,y,z range (A): 46.08400 44.75700 46.75000 scale (grids/A): 2.284492 object centre (A): 31.94700 13.50650 20.29900 number of atom coordinates read : 2117 total number of charged atoms : 1976 net assigned charge : -6.746984 assigned positive charge : 317.4199 centred at (gu) : 88.68855 91.89440 90.54591 assigned negative charge : -324.1670 centred at (gu) : 88.70470 92.17616 91.06767 start vw surface at 0.1300000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87365 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18901 grid for indexing accessible points = 1.400000 m= 36065 mr = 60075 m= 8369 mr = 27674 m= 1023 mr = 5979 m= 40 mr = 612 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 4608 time to turn everything in is 0.8900000 number of dielectric boundary points 38518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 15769 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) : 0.7614973 object centre at (A) : 31.94700 13.50650 20.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6120924E-03 -0.1466354 midg,1,midg; midg,igrid,midg -3.0146684E-02 -5.7174619E-02 1,midg,midg; igrid,midg,midg -2.8884299E-02 -3.4473788E-02 gauss-seidel spectral radius is 0.9989741 estimated iterations to convergence 247 setup time was (sec) 1.510000 now iterating at: 12:14:03 rms-change max change #iterations 5.359962 230.8969 at 10iterations 2.767091 88.66469 at 20iterations 1.427467 37.65323 at 30iterations 0.7390339 20.29213 at 40iterations 0.3821810 10.80145 at 50iterations 0.1979388 5.744442 at 60iterations 0.1026512 2.684167 at 70iterations 5.3249661E-02 1.361397 at 80iterations 2.7491521E-02 0.7509995 at 90iterations 1.4256065E-02 0.3924966 at 100iterations 7.3798634E-03 0.1927967 at 110iterations 3.7984794E-03 0.1017513 at 120iterations finished qdiffx linear iterations at : 12:14:22 total time elapsed so far: 20.25000 # loops : 120 mean,max change (kT/e) : 3.7984794E-03 0.1017513 energy calculations done at 20.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.41000 DelPhi exited at 12:14:22 20.415u 0.882s 0:21.71 98.0% 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 12:14:23 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.426738 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): 8.905001 54.98900 ymin,ymax (A): -8.872000 35.88500 zmin,zma (A): -3.076000 43.67400 x,y,z range (A): 46.08400 44.75700 46.75000 scale (grids/A): 3.426738 object centre (A): 31.94700 13.50650 20.29900 number of atom coordinates read : 2117 total number of charged atoms : 1976 net assigned charge : -6.746984 assigned positive charge : 317.4199 centred at (gu) : 88.03274 92.84162 90.81887 assigned negative charge : -324.1670 centred at (gu) : 88.05698 93.26424 91.60155 start vw surface at 0.1100000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 200707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18901 grid for indexing accessible points = 1.400000 m= 108930 mr = 144237 m= 48708 mr = 90715 m= 16445 mr = 40876 m= 3925 mr = 13265 m= 689 mr = 3046 m= 39 mr = 510 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 1.400000 no. cavity mid-points inaccessible to solvent = 15409 time to turn everything in is 2.610000 number of dielectric boundary points 86783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.850000 number of grid points assigned charge 15808 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) : 2.284492 object centre at (A) : 31.94700 13.50650 20.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5869662E-02 -1.434599 midg,1,midg; midg,igrid,midg -0.2594155 -0.2710558 1,midg,midg; igrid,midg,midg -0.3261487 -0.4390231 gauss-seidel spectral radius is 0.9993320 estimated iterations to convergence 305 setup time was (sec) 3.180000 now iterating at: 12:14:26 rms-change max change #iterations 11.42108 289.6748 at 10iterations 6.757916 110.3935 at 20iterations 4.014207 88.71855 at 30iterations 2.377059 41.51324 at 40iterations 1.408464 23.53807 at 50iterations 0.8310347 13.22715 at 60iterations 0.4918762 7.598008 at 70iterations 0.2909739 4.591583 at 80iterations 0.1721020 2.684289 at 90iterations 0.1014341 1.612483 at 100iterations 5.9874017E-02 1.063995 at 110iterations 3.5353158E-02 0.5266438 at 120iterations 2.0878565E-02 0.3306003 at 130iterations 1.2343382E-02 0.2019372 at 140iterations 7.2752144E-03 0.1100383 at 150iterations 4.3126768E-03 6.7005157E-02 at 160iterations 2.5419232E-03 3.9266586E-02 at 170iterations 1.5051762E-03 2.3353577E-02 at 180iterations finished qdiffx linear iterations at : 12:14:55 total time elapsed so far: 31.93000 # loops : 180 mean,max change (kT/e) : 1.5051762E-03 2.3353577E-02 energy calculations done at 31.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 32.09000 DelPhi exited at 12:14:56 32.099u 0.770s 0:33.33 98.5% 0+0k 0+0io 0pf+0w