Sat Oct 8 18:27:24 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 18:27:24 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3409 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: 0.5682091 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): 50.53900 110.5180 ymin,ymax (A): -19.16300 41.60100 zmin,zma (A): -34.58900 28.06400 x,y,z range (A): 59.97900 60.76400 62.65300 scale (grids/A): 0.5682091 object centre (A): 80.52850 11.21900 -3.262499 number of atom coordinates read : 3409 total number of charged atoms : 3266 net assigned charge : 5.000032 assigned positive charge : 512.3943 centred at (gu) : 88.52814 89.43362 90.88559 assigned negative charge : -507.3958 centred at (gu) : 88.48934 89.55348 90.86819 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7327 nv = 96 ne = 84 npr = 67911 no. pairs analyzed = 67911 no. exposed pairs = 4488 no. arc points = 32197 no. surface atoms = 1498 nbur = 1911 mkacc time = 0.1500000 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= 364 mr = 3721 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3600000 number of dielectric boundary points 3945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3215 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9404 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4501568E-10 1.2377860E-09 midg,1,midg; midg,igrid,midg 3.0916771E-09 -1.1561143E-09 1,midg,midg; igrid,midg,midg 6.4651569E-11 9.6420638E-10 gauss-seidel spectral radius is 0.9840622 estimated iterations to convergence 65 setup time was (sec) 0.6100000 now iterating at: 18:27:25 rms-change max change #iterations 9.6117996E-02 14.28111 at 10iterations 7.2779646E-03 1.308247 at 20iterations 6.4920378E-04 9.4490051E-02 at 30iterations 9.3634138E-05 1.3027191E-02 at 40iterations 1.9450201E-05 2.6893616E-03 at 50iterations finished qdiffx linear iterations at : 18:27:28 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.9450201E-05 2.6893616E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 18:27:28 3.415u 0.190s 0:03.90 92.3% 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 Sat Oct 8 2011 at 18:27:28 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3409 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: 1.704627 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): 50.53900 110.5180 ymin,ymax (A): -19.16300 41.60100 zmin,zma (A): -34.58900 28.06400 x,y,z range (A): 59.97900 60.76400 62.65300 scale (grids/A): 1.704627 object centre (A): 80.52850 11.21900 -3.262499 number of atom coordinates read : 3409 total number of charged atoms : 3266 net assigned charge : 5.000032 assigned positive charge : 512.3943 centred at (gu) : 85.58344 88.29973 92.65566 assigned negative charge : -507.3958 centred at (gu) : 85.46783 88.66028 92.60411 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32197 grid for indexing accessible points = 1.400000 m= 27073 mr = 52652 m= 3570 mr = 18743 m= 113 mr = 1951 m= 3 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2229 time to turn everything in is 0.5900000 number of dielectric boundary points 36886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 25226 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) : 0.5682091 object centre at (A) : 80.52850 11.21900 -3.262499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0450249E-02 2.1081375E-02 midg,1,midg; midg,igrid,midg 1.3471929E-02 -1.1707552E-02 1,midg,midg; igrid,midg,midg -4.3325196E-03 2.6367677E-03 gauss-seidel spectral radius is 0.9983907 estimated iterations to convergence 198 setup time was (sec) 0.9000000 now iterating at: 18:27:29 rms-change max change #iterations 3.943818 153.3556 at 10iterations 1.720850 63.27872 at 20iterations 0.7546426 23.17547 at 30iterations 0.3303221 12.20713 at 40iterations 0.1447410 5.057146 at 50iterations 6.3230947E-02 2.075487 at 60iterations 2.7792979E-02 0.9194717 at 70iterations 1.2154786E-02 0.4038849 at 80iterations 5.3404793E-03 0.1618938 at 90iterations 2.3650900E-03 8.1747055E-02 at 100iterations 1.0372252E-03 3.2517910E-02 at 110iterations 4.5581325E-04 1.5835047E-02 at 120iterations finished qdiffx linear iterations at : 18:27:36 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 4.5581325E-04 1.5835047E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 18:27:36 7.833u 0.269s 0:08.41 96.1% 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 18:27:37 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3409 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.556941 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): 50.53900 110.5180 ymin,ymax (A): -19.16300 41.60100 zmin,zma (A): -34.58900 28.06400 x,y,z range (A): 59.97900 60.76400 62.65300 scale (grids/A): 2.556941 object centre (A): 80.52850 11.21900 -3.262499 number of atom coordinates read : 3409 total number of charged atoms : 3266 net assigned charge : 5.000032 assigned positive charge : 512.3943 centred at (gu) : 83.37501 87.44935 93.98314 assigned negative charge : -507.3958 centred at (gu) : 83.20153 87.99039 93.90620 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 183837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32197 grid for indexing accessible points = 1.400000 m= 88774 mr = 128677 m= 29897 mr = 69758 m= 6007 mr = 22996 m= 453 mr = 4136 m= 6 mr = 186 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 7701 time to turn everything in is 1.430000 number of dielectric boundary points 83221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 26115 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) : 1.704627 object centre at (A) : 80.52850 11.21900 -3.262499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1690720 -5.3253397E-02 midg,1,midg; midg,igrid,midg 0.1814053 -0.1736795 1,midg,midg; igrid,midg,midg 0.1535595 -5.6515038E-03 gauss-seidel spectral radius is 0.9992139 estimated iterations to convergence 282 setup time was (sec) 1.760000 now iterating at: 18:27:38 rms-change max change #iterations 10.04446 330.8712 at 10iterations 5.908310 143.0882 at 20iterations 3.419242 83.04633 at 30iterations 1.972801 45.63428 at 40iterations 1.134526 22.49689 at 50iterations 0.6493092 13.29992 at 60iterations 0.3698803 7.638542 at 70iterations 0.2106400 4.155769 at 80iterations 0.1196618 2.392025 at 90iterations 6.7952156E-02 1.260208 at 100iterations 3.8567666E-02 0.7219584 at 110iterations 2.1829586E-02 0.4001503 at 120iterations 1.2367574E-02 0.2429943 at 130iterations 7.0111975E-03 0.1236982 at 140iterations 3.9590602E-03 7.2454453E-02 at 150iterations 2.2438283E-03 4.4952393E-02 at 160iterations 1.2678357E-03 2.1902561E-02 at 170iterations 7.1663328E-04 1.3015747E-02 at 180iterations finished qdiffx linear iterations at : 18:27:49 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 7.1663328E-04 1.3015747E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 18:27:50 12.620u 0.226s 0:13.14 97.7% 0+0k 0+0io 0pf+0w