Sun Oct 9 01:48:28 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 Sun Oct 9 2011 at 01:48:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3290 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: 0.5717865 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): -24.23900 37.61700 ymin,ymax (A): 20.39000 79.70300 zmin,zma (A): -30.42100 31.84000 x,y,z range (A): 61.85600 59.31300 62.26100 scale (grids/A): 0.5717865 object centre (A): 6.689000 50.04650 0.7095003 number of atom coordinates read : 3290 total number of charged atoms : 3146 net assigned charge : 12.50004 assigned positive charge : 484.0597 centred at (gu) : 91.77111 89.55719 88.13856 assigned negative charge : -471.5613 centred at (gu) : 91.84122 89.34713 88.04939 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7486 nv = 96 ne = 84 npr = 62854 no. pairs analyzed = 62854 no. exposed pairs = 4551 no. arc points = 32615 no. surface atoms = 1513 nbur = 1777 mkacc time = 0.1600000 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= 356 mr = 3732 m= 4 mr = 16 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 0.3700000 number of dielectric boundary points 4098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3359 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9425 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5856293E-10 2.3736717E-09 midg,1,midg; midg,igrid,midg -1.8753292E-09 5.1374558E-09 1,midg,midg; igrid,midg,midg 2.2083304E-09 1.2712904E-09 gauss-seidel spectral radius is 0.9842610 estimated iterations to convergence 65 setup time was (sec) 0.6300000 now iterating at: 01:48:30 rms-change max change #iterations 9.4867535E-02 14.00465 at 10iterations 7.0272805E-03 1.177574 at 20iterations 5.6054979E-04 7.6774597E-02 at 30iterations 5.9062364E-05 1.1802673E-02 at 40iterations 1.2672028E-05 3.1948090E-03 at 50iterations finished qdiffx linear iterations at : 01:48:33 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 1.2672028E-05 3.1948090E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 01:48:34 4.557u 0.409s 0:05.24 94.4% 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 Sun Oct 9 2011 at 01:48:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3290 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: 1.715359 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): -24.23900 37.61700 ymin,ymax (A): 20.39000 79.70300 zmin,zma (A): -30.42100 31.84000 x,y,z range (A): 61.85600 59.31300 62.26100 scale (grids/A): 1.715359 object centre (A): 6.689000 50.04650 0.7095003 number of atom coordinates read : 3290 total number of charged atoms : 3146 net assigned charge : 12.50004 assigned positive charge : 484.0597 centred at (gu) : 95.31213 88.67079 84.41489 assigned negative charge : -471.5613 centred at (gu) : 95.52334 88.04135 84.14789 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32615 grid for indexing accessible points = 1.400000 m= 27638 mr = 53949 m= 3600 mr = 19171 m= 134 mr = 1944 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 904 time to turn everything in is 0.6700000 number of dielectric boundary points 38012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 24388 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) : 0.5717865 object centre at (A) : 6.689000 50.04650 0.7095003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7205447E-02 4.9332988E-02 midg,1,midg; midg,igrid,midg -1.8429833E-02 1.6258756E-02 1,midg,midg; igrid,midg,midg 9.9139158E-03 1.8179193E-02 gauss-seidel spectral radius is 0.9984133 estimated iterations to convergence 199 setup time was (sec) 0.9600000 now iterating at: 01:48:35 rms-change max change #iterations 3.836847 215.2154 at 10iterations 1.672780 62.42244 at 20iterations 0.7368428 23.61691 at 30iterations 0.3243402 9.787455 at 40iterations 0.1430366 4.550154 at 50iterations 6.2932678E-02 2.095345 at 60iterations 2.7784502E-02 0.8992882 at 70iterations 1.2220579E-02 0.4521408 at 80iterations 5.4088780E-03 0.1745872 at 90iterations 2.3903928E-03 7.7244759E-02 at 100iterations 1.0595478E-03 3.4055710E-02 at 110iterations 4.6821497E-04 1.5251160E-02 at 120iterations finished qdiffx linear iterations at : 01:48:45 total time elapsed so far: 10.53000 # loops : 120 mean,max change (kT/e) : 4.6821497E-04 1.5251160E-02 energy calculations done at 10.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 01:48:45 10.696u 0.464s 0:11.54 96.6% 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 Sun Oct 9 2011 at 01:48:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3290 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: 2.573039 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): -24.23900 37.61700 ymin,ymax (A): 20.39000 79.70300 zmin,zma (A): -30.42100 31.84000 x,y,z range (A): 61.85600 59.31300 62.26100 scale (grids/A): 2.573039 object centre (A): 6.689000 50.04650 0.7095003 number of atom coordinates read : 3290 total number of charged atoms : 3146 net assigned charge : 12.50004 assigned positive charge : 484.0597 centred at (gu) : 97.96806 88.00604 81.62214 assigned negative charge : -471.5613 centred at (gu) : 98.28491 87.06199 81.22174 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 189240 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32615 grid for indexing accessible points = 1.400000 m= 91440 mr = 132161 m= 29926 mr = 72033 m= 6043 mr = 22865 m= 615 mr = 4140 m= 13 mr = 327 m= 0 mr = 2 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 2739 time to turn everything in is 1.690000 number of dielectric boundary points 85749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 25158 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) : 1.715359 object centre at (A) : 6.689000 50.04650 0.7095003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4275568 0.7254834 midg,1,midg; midg,igrid,midg -0.1680745 0.2172690 1,midg,midg; igrid,midg,midg 4.2293284E-02 0.1735828 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 2.030000 now iterating at: 01:48:48 rms-change max change #iterations 9.823075 312.6607 at 10iterations 5.744328 138.8264 at 20iterations 3.335377 78.32484 at 30iterations 1.920738 39.34370 at 40iterations 1.104232 21.06478 at 50iterations 0.6316100 12.06216 at 60iterations 0.3612672 7.164152 at 70iterations 0.2065848 4.338871 at 80iterations 0.1173949 2.542469 at 90iterations 6.6818230E-02 1.222078 at 100iterations 3.8063742E-02 0.7302933 at 110iterations 2.1620426E-02 0.3825550 at 120iterations 1.2308738E-02 0.2445879 at 130iterations 6.9738454E-03 0.1290627 at 140iterations 3.9588814E-03 6.9440365E-02 at 150iterations 2.2493275E-03 4.1574478E-02 at 160iterations 1.2790166E-03 2.3625791E-02 at 170iterations 7.2740269E-04 1.4231920E-02 at 180iterations finished qdiffx linear iterations at : 01:49:04 total time elapsed so far: 18.63000 # loops : 180 mean,max change (kT/e) : 7.2740269E-04 1.4231920E-02 energy calculations done at 18.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.80000 DelPhi exited at 01:49:05 18.800u 0.499s 0:19.64 98.2% 0+0k 0+0io 0pf+0w