Mon Oct 10 14:39:32 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 14:39:32 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 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: 0.6407834 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): -44.15500 5.517000 ymin,ymax (A): -31.54400 24.01300 zmin,zma (A): -37.21600 14.59400 x,y,z range (A): 49.67200 55.55700 51.81000 scale (grids/A): 0.6407834 object centre (A): -19.31900 -3.765499 -11.31100 number of atom coordinates read : 2283 total number of charged atoms : 2127 net assigned charge : -0.9999933 assigned positive charge : 334.9893 centred at (gu) : 90.59021 89.41969 90.38805 assigned negative charge : -335.9896 centred at (gu) : 90.80345 89.55470 90.33508 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6527 nv = 96 ne = 84 npr = 45273 no. pairs analyzed = 45273 no. exposed pairs = 3102 no. arc points = 21676 no. surface atoms = 1039 nbur = 1244 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3367 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2095 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.3593353E-09 4.3743085E-09 midg,1,midg; midg,igrid,midg 1.3977463E-08 -1.3714073E-08 1,midg,midg; igrid,midg,midg 1.7645652E-08 -2.7220500E-08 gauss-seidel spectral radius is 0.9873626 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 14:39:33 rms-change max change #iterations 0.1341849 20.97066 at 10iterations 1.3212989E-02 1.927955 at 20iterations 1.3395078E-03 0.1992950 at 30iterations 1.3143317E-04 1.9380569E-02 at 40iterations 1.3169492E-05 2.0217896E-03 at 50iterations finished qdiffx linear iterations at : 14:39:37 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 1.3169492E-05 2.0217896E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 14:39:38 4.561u 0.397s 0:06.03 82.0% 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 14:39:38 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 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: 1.922350 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): -44.15500 5.517000 ymin,ymax (A): -31.54400 24.01300 zmin,zma (A): -37.21600 14.59400 x,y,z range (A): 49.67200 55.55700 51.81000 scale (grids/A): 1.922350 object centre (A): -19.31900 -3.765499 -11.31100 number of atom coordinates read : 2283 total number of charged atoms : 2127 net assigned charge : -0.9999933 assigned positive charge : 334.9893 centred at (gu) : 91.77040 88.25876 91.16354 assigned negative charge : -335.9896 centred at (gu) : 92.41021 88.66396 91.00525 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21676 grid for indexing accessible points = 1.400000 m= 24305 mr = 47107 m= 3564 mr = 17016 m= 169 mr = 1916 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 31936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 16762 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) : 0.6407834 object centre at (A) : -19.31900 -3.765499 -11.31100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6173985E-02 4.5564882E-03 midg,1,midg; midg,igrid,midg 1.2396139E-02 3.0618322E-03 1,midg,midg; igrid,midg,midg 7.1134274E-03 -2.8753158E-02 gauss-seidel spectral radius is 0.9986380 estimated iterations to convergence 215 setup time was (sec) 0.9000000 now iterating at: 14:39:40 rms-change max change #iterations 3.995886 164.6534 at 10iterations 1.866572 83.01751 at 20iterations 0.8726264 31.40054 at 30iterations 0.4088832 13.24801 at 40iterations 0.1903800 6.135290 at 50iterations 8.9530237E-02 3.380806 at 60iterations 4.1914251E-02 1.418919 at 70iterations 1.9606339E-02 0.6560290 at 80iterations 9.1514541E-03 0.3047523 at 90iterations 4.2960178E-03 0.1398621 at 100iterations 2.0065138E-03 7.2928905E-02 at 110iterations 9.4153726E-04 3.0174255E-02 at 120iterations finished qdiffx linear iterations at : 14:39:50 total time elapsed so far: 11.19000 # loops : 120 mean,max change (kT/e) : 9.4153726E-04 3.0174255E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 14:39:50 11.353u 0.446s 0:12.12 97.2% 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 14:39:51 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 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: 2.883525 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): -44.15500 5.517000 ymin,ymax (A): -31.54400 24.01300 zmin,zma (A): -37.21600 14.59400 x,y,z range (A): 49.67200 55.55700 51.81000 scale (grids/A): 2.883525 object centre (A): -19.31900 -3.765499 -11.31100 number of atom coordinates read : 2283 total number of charged atoms : 2127 net assigned charge : -0.9999933 assigned positive charge : 334.9893 centred at (gu) : 92.65546 87.38806 91.74533 assigned negative charge : -335.9896 centred at (gu) : 93.61532 87.99586 91.50785 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 161578 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21676 grid for indexing accessible points = 1.400000 m= 79813 mr = 114532 m= 27393 mr = 63691 m= 6032 mr = 20774 m= 672 mr = 4075 m= 49 mr = 382 m= 0 mr = 31 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 72052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 17016 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) : 1.922350 object centre at (A) : -19.31900 -3.765499 -11.31100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2591726 4.6270736E-02 midg,1,midg; midg,igrid,midg 5.1588425E-03 9.2229173E-02 1,midg,midg; igrid,midg,midg -2.2598638E-03 -0.2568953 gauss-seidel spectral radius is 0.9992640 estimated iterations to convergence 291 setup time was (sec) 1.940000 now iterating at: 14:39:53 rms-change max change #iterations 9.577986 373.2363 at 10iterations 5.659626 133.0375 at 20iterations 3.320082 71.09900 at 30iterations 1.935900 48.24003 at 40iterations 1.125091 23.26785 at 50iterations 0.6533305 14.88002 at 60iterations 0.3786676 7.789436 at 70iterations 0.2187894 4.585808 at 80iterations 0.1264637 2.340004 at 90iterations 7.3039718E-02 1.375034 at 100iterations 4.2137522E-02 0.7520084 at 110iterations 2.4250505E-02 0.5057586 at 120iterations 1.3954019E-02 0.2515488 at 130iterations 8.0540003E-03 0.1573038 at 140iterations 4.6359561E-03 8.3704948E-02 at 150iterations 2.6671209E-03 5.2316666E-02 at 160iterations 1.5355517E-03 2.7680039E-02 at 170iterations 8.8180986E-04 1.8646717E-02 at 180iterations finished qdiffx linear iterations at : 14:40:10 total time elapsed so far: 19.03000 # loops : 180 mean,max change (kT/e) : 8.8180986E-04 1.8646717E-02 energy calculations done at 19.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.19000 DelPhi exited at 14:40:11 19.191u 0.481s 0:20.26 97.0% 0+0k 0+0io 0pf+0w