Mon Oct 10 13:58:29 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 13:58:29 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 !!! 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: ZN5 504 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6243861 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): -31.30600 17.69700 ymin,ymax (A): -23.78700 22.76100 zmin,zma (A): -12.46700 44.54900 x,y,z range (A): 49.00300 46.54800 57.01600 scale (grids/A): 0.6243861 object centre (A): -6.804500 -0.5129995 16.04100 number of atom coordinates read : 2590 total number of charged atoms : 2468 net assigned charge : 4.000009 assigned positive charge : 393.6960 centred at (gu) : 88.35213 89.20795 89.76847 assigned negative charge : -389.6965 centred at (gu) : 88.24625 89.26747 89.66299 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6516 nv = 96 ne = 84 npr = 54032 no. pairs analyzed = 54032 no. exposed pairs = 2969 no. arc points = 21467 no. surface atoms = 999 nbur = 1591 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3598 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 116 time to turn everything in is 0.3100000 number of dielectric boundary points 3194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2147 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4837289E-09 1.1093113E-08 midg,1,midg; midg,igrid,midg 9.8310897E-09 -5.7095140E-10 1,midg,midg; igrid,midg,midg -6.3112742E-09 8.1801899E-09 gauss-seidel spectral radius is 0.9867100 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 13:58:30 rms-change max change #iterations 0.1329241 24.51929 at 10iterations 1.2249746E-02 1.825862 at 20iterations 1.1682045E-03 0.1784973 at 30iterations 1.0825379E-04 1.8867493E-02 at 40iterations 1.0207093E-05 1.4610291E-03 at 50iterations finished qdiffx linear iterations at : 13:58:34 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 1.0207093E-05 1.4610291E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 13:58:35 4.669u 0.394s 0:05.50 91.8% 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 13:58:35 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 !!! 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: ZN5 504 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.873158 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): -31.30600 17.69700 ymin,ymax (A): -23.78700 22.76100 zmin,zma (A): -12.46700 44.54900 x,y,z range (A): 49.00300 46.54800 57.01600 scale (grids/A): 1.873158 object centre (A): -6.804500 -0.5129995 16.04100 number of atom coordinates read : 2590 total number of charged atoms : 2468 net assigned charge : 4.000009 assigned positive charge : 393.6960 centred at (gu) : 85.05583 87.62341 89.30493 assigned negative charge : -389.6965 centred at (gu) : 84.73852 87.80212 88.98873 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21467 grid for indexing accessible points = 1.400000 m= 24060 mr = 50050 m= 3276 mr = 17627 m= 125 mr = 1962 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 5261 time to turn everything in is 0.5600000 number of dielectric boundary points 29390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19402 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) : 0.6243861 object centre at (A) : -6.804500 -0.5129995 16.04100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7268158E-02 1.4897097E-02 midg,1,midg; midg,igrid,midg 1.5712351E-02 4.5532379E-03 1,midg,midg; igrid,midg,midg -1.8454865E-03 3.9599922E-02 gauss-seidel spectral radius is 0.9985857 estimated iterations to convergence 211 setup time was (sec) 0.8800000 now iterating at: 13:58:36 rms-change max change #iterations 4.071652 182.6055 at 10iterations 1.879876 65.20103 at 20iterations 0.8656330 31.99091 at 30iterations 0.3998538 13.65753 at 40iterations 0.1855826 5.621045 at 50iterations 8.5607067E-02 2.921898 at 60iterations 3.9697565E-02 1.285515 at 70iterations 1.8349530E-02 0.6140175 at 80iterations 8.4755495E-03 0.2959461 at 90iterations 3.9148545E-03 0.1209869 at 100iterations 1.8064098E-03 5.7480574E-02 at 110iterations 8.3611236E-04 2.5573730E-02 at 120iterations finished qdiffx linear iterations at : 13:58:46 total time elapsed so far: 10.91000 # loops : 120 mean,max change (kT/e) : 8.3611236E-04 2.5573730E-02 energy calculations done at 10.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 13:58:47 11.097u 0.475s 0:11.87 97.3% 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 13:58:47 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 !!! 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: ZN5 504 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.809738 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): -31.30600 17.69700 ymin,ymax (A): -23.78700 22.76100 zmin,zma (A): -12.46700 44.54900 x,y,z range (A): 49.00300 46.54800 57.01600 scale (grids/A): 2.809738 object centre (A): -6.804500 -0.5129995 16.04100 number of atom coordinates read : 2590 total number of charged atoms : 2468 net assigned charge : 4.000009 assigned positive charge : 393.6960 centred at (gu) : 82.58364 86.43498 88.95744 assigned negative charge : -389.6965 centred at (gu) : 82.10769 86.70307 88.48302 start vw surface at 0.1100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 165946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21467 grid for indexing accessible points = 1.400000 m= 80785 mr = 121296 m= 26322 mr = 66282 m= 5613 mr = 20967 m= 629 mr = 4130 m= 22 mr = 383 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 17720 time to turn everything in is 1.470000 number of dielectric boundary points 66249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 19740 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) : 1.873158 object centre at (A) : -6.804500 -0.5129995 16.04100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1002954 0.1679266 midg,1,midg; midg,igrid,midg 0.1798178 2.8352719E-02 1,midg,midg; igrid,midg,midg -1.0362288E-02 0.5191759 gauss-seidel spectral radius is 0.9992391 estimated iterations to convergence 286 setup time was (sec) 1.830000 now iterating at: 13:58:49 rms-change max change #iterations 9.559687 292.0209 at 10iterations 5.501336 160.1729 at 20iterations 3.144734 61.97015 at 30iterations 1.796138 34.53302 at 40iterations 1.025634 24.26279 at 50iterations 0.5836973 12.44973 at 60iterations 0.3338384 6.580907 at 70iterations 0.1902308 3.723559 at 80iterations 0.1084631 2.665321 at 90iterations 6.1794583E-02 1.221277 at 100iterations 3.5169858E-02 0.7173996 at 110iterations 2.0070326E-02 0.3785129 at 120iterations 1.1425648E-02 0.2333584 at 130iterations 6.5238625E-03 0.1283178 at 140iterations 3.7125645E-03 6.7227721E-02 at 150iterations 2.1210820E-03 4.0046692E-02 at 160iterations 1.2095635E-03 2.2423029E-02 at 170iterations 6.9000956E-04 1.2811661E-02 at 180iterations finished qdiffx linear iterations at : 13:59:15 total time elapsed so far: 27.85000 # loops : 180 mean,max change (kT/e) : 6.9000956E-04 1.2811661E-02 energy calculations done at 27.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.05000 DelPhi exited at 13:59:16 28.056u 0.586s 0:29.17 98.1% 0+0k 0+0io 0pf+0w