Wed Dec 28 11:01:28 PST 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 Wed Dec 28 2011 at 11:01:28 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1967 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 0.5867809 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): -35.16900 9.790999 ymin,ymax (A): 1.126000 41.17800 zmin,zma (A): -1.810000 58.86000 x,y,z range (A): 44.96000 40.05200 60.67000 scale (grids/A): 0.5867809 object centre (A): -12.68900 21.15200 28.52500 number of atom coordinates read : 1967 total number of charged atoms : 1834 net assigned charge : 0.6810054 assigned positive charge : 289.0541 centred at (gu) : 90.49722 89.61692 89.53271 assigned negative charge : -288.3733 centred at (gu) : 90.41723 89.74078 89.51501 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4527 nv = 96 ne = 84 npr = 40417 no. pairs analyzed = 40417 no. exposed pairs = 2437 no. arc points = 16977 no. surface atoms = 828 nbur = 1139 mkacc time = 0.1100000 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 = 1.484000 m= 214 mr = 2476 m= 0 mr = 16 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1759 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 5582 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6021244E-10 4.3945955E-10 midg,1,midg; midg,igrid,midg 2.5740661E-09 -1.8889306E-09 1,midg,midg; igrid,midg,midg -1.1256828E-09 1.7851116E-09 gauss-seidel spectral radius is 0.9849220 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 11:01:29 rms-change max change #iterations 8.4950477E-02 18.95417 at 10iterations 6.7654201E-03 1.493256 at 20iterations 5.3279073E-04 0.1090403 at 30iterations 4.2447122E-05 6.6661835E-03 at 40iterations 3.4388702E-06 6.0558319E-04 at 50iterations finished qdiffx linear iterations at : 11:01:33 total time elapsed so far: 4.930000 # loops : 50 mean,max change (kT/e) : 3.4388702E-06 6.0558319E-04 energy calculations done at 4.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.120000 DelPhi exited at 11:01:34 5.127u 0.437s 0:06.23 89.0% 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 Wed Dec 28 2011 at 11:01:34 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1967 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 1.760343 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): -35.16900 9.790999 ymin,ymax (A): 1.126000 41.17800 zmin,zma (A): -1.810000 58.86000 x,y,z range (A): 44.96000 40.05200 60.67000 scale (grids/A): 1.760343 object centre (A): -12.68900 21.15200 28.52500 number of atom coordinates read : 1967 total number of charged atoms : 1834 net assigned charge : 0.6810054 assigned positive charge : 289.0541 centred at (gu) : 91.49169 88.85104 88.59824 assigned negative charge : -288.3733 centred at (gu) : 91.25193 89.22265 88.54536 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 48847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 17206 mr = 33364 m= 2180 mr = 12965 m= 70 mr = 1282 m= 1 mr = 18 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 0.4800000 number of dielectric boundary points 20675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14271 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) : 0.5867809 object centre at (A) : -12.68900 21.15200 28.52500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5598969E-02 2.0166639E-02 midg,1,midg; midg,igrid,midg -3.5557526E-04 -9.6830865E-03 1,midg,midg; igrid,midg,midg -4.4593778E-03 -4.9752099E-03 gauss-seidel spectral radius is 0.9983249 estimated iterations to convergence 194 setup time was (sec) 0.7800000 now iterating at: 11:01:35 rms-change max change #iterations 3.046201 179.7551 at 10iterations 1.312031 50.80252 at 20iterations 0.5671026 22.87733 at 30iterations 0.2452635 9.927742 at 40iterations 0.1055008 4.299255 at 50iterations 4.5539897E-02 1.889492 at 60iterations 1.9720981E-02 0.8334923 at 70iterations 8.4502865E-03 0.3226128 at 80iterations 3.6500511E-03 0.1474886 at 90iterations 1.5825552E-03 6.2247396E-02 at 100iterations 6.8182603E-04 2.6596069E-02 at 110iterations 2.9457672E-04 1.1367798E-02 at 120iterations finished qdiffx linear iterations at : 11:01:46 total time elapsed so far: 11.62000 # loops : 120 mean,max change (kT/e) : 2.9457672E-04 1.1367798E-02 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 11:01:47 11.822u 0.328s 0:12.56 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 Wed Dec 28 2011 at 11:01:47 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1967 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 2.640514 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): -35.16900 9.790999 ymin,ymax (A): 1.126000 41.17800 zmin,zma (A): -1.810000 58.86000 x,y,z range (A): 44.96000 40.05200 60.67000 scale (grids/A): 2.640514 object centre (A): -12.68900 21.15200 28.52500 number of atom coordinates read : 1967 total number of charged atoms : 1834 net assigned charge : 0.6810054 assigned positive charge : 289.0541 centred at (gu) : 92.23759 88.27650 87.89742 assigned negative charge : -288.3733 centred at (gu) : 91.87807 88.83397 87.81807 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 113002 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 56686 mr = 80814 m= 19250 mr = 46864 m= 3615 mr = 15759 m= 355 mr = 2651 m= 8 mr = 235 m= 0 mr = 2 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 46591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 14665 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) : 1.760343 object centre at (A) : -12.68900 21.15200 28.52500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2830786 0.1714337 midg,1,midg; midg,igrid,midg -3.4637105E-02 -0.1401458 1,midg,midg; igrid,midg,midg -7.2732903E-02 -0.1097656 gauss-seidel spectral radius is 0.9991497 estimated iterations to convergence 271 setup time was (sec) 1.570000 now iterating at: 11:01:49 rms-change max change #iterations 7.377411 263.7379 at 10iterations 4.092308 129.8304 at 20iterations 2.268662 63.54693 at 30iterations 1.250971 32.91974 at 40iterations 0.6884874 16.82242 at 50iterations 0.3798791 8.913181 at 60iterations 0.2083003 4.910063 at 70iterations 0.1148859 3.232508 at 80iterations 6.3298091E-02 1.362547 at 90iterations 3.4860555E-02 0.8158159 at 100iterations 1.9142063E-02 0.4919000 at 110iterations 1.0578984E-02 0.2547112 at 120iterations 5.8009624E-03 0.1386052 at 130iterations 3.1884508E-03 6.8861008E-02 at 140iterations 1.7572911E-03 4.0280819E-02 at 150iterations 9.6617150E-04 2.2192001E-02 at 160iterations 5.3187500E-04 1.2477875E-02 at 170iterations 2.9323794E-04 6.4729452E-03 at 180iterations finished qdiffx linear iterations at : 11:02:05 total time elapsed so far: 17.83000 # loops : 180 mean,max change (kT/e) : 2.9323794E-04 6.4729452E-03 energy calculations done at 17.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.03000 DelPhi exited at 11:02:06 18.031u 0.575s 0:19.41 95.8% 0+0k 0+0io 0pf+0w