Wed Dec 28 11:02:06 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+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 Wed Dec 28 2011 at 11:02:07 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 0.6410372 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): -3.919000 35.29600 ymin,ymax (A): -4.302000 48.73500 zmin,zma (A): -24.13700 31.39800 x,y,z range (A): 39.21500 53.03700 55.53500 scale (grids/A): 0.6410372 object centre (A): 15.68850 22.21650 3.630500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 290.6260 centred at (gu) : 90.10718 92.79859 90.01749 assigned negative charge : -286.6263 centred at (gu) : 90.16505 92.90337 89.95312 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5581 nv = 96 ne = 84 npr = 40147 no. pairs analyzed = 40147 no. exposed pairs = 2393 no. arc points = 16979 no. surface atoms = 818 nbur = 1144 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 274 mr = 3161 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2600000 number of dielectric boundary points 2663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1692 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6493 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6010785E-10 1.1905708E-08 midg,1,midg; midg,igrid,midg 8.5326537E-09 -6.0562608E-09 1,midg,midg; igrid,midg,midg 1.1045251E-08 1.1582607E-09 gauss-seidel spectral radius is 0.9873359 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 11:02:08 rms-change max change #iterations 0.1255348 18.72334 at 10iterations 1.2521211E-02 1.815205 at 20iterations 1.2581031E-03 0.2195148 at 30iterations 1.2443781E-04 2.0254135E-02 at 40iterations 1.2349137E-05 1.8901825E-03 at 50iterations finished qdiffx linear iterations at : 11:02:13 total time elapsed so far: 4.800000 # loops : 50 mean,max change (kT/e) : 1.2349137E-05 1.8901825E-03 energy calculations done at 4.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.970000 DelPhi exited at 11:02:14 4.970u 0.368s 0:06.28 84.8% 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 11:02:14 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 1.923112 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): -3.919000 35.29600 ymin,ymax (A): -4.302000 48.73500 zmin,zma (A): -24.13700 31.39800 x,y,z range (A): 39.21500 53.03700 55.53500 scale (grids/A): 1.923112 object centre (A): 15.68850 22.21650 3.630500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 290.6260 centred at (gu) : 90.32159 98.39541 90.05239 assigned negative charge : -286.6263 centred at (gu) : 90.49528 98.71044 89.85949 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 22642 mr = 41844 m= 3363 mr = 17484 m= 156 mr = 2188 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2342 time to turn everything in is 0.5100000 number of dielectric boundary points 24466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 14431 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) : 0.6410372 object centre at (A) : 15.68850 22.21650 3.630500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7442954E-02 2.3070985E-02 midg,1,midg; midg,igrid,midg 3.4914024E-02 1.1179608E-03 1,midg,midg; igrid,midg,midg 3.6324682E-03 -1.2489655E-03 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.8100000 now iterating at: 11:02:15 rms-change max change #iterations 3.646726 171.1531 at 10iterations 1.684526 64.20957 at 20iterations 0.7782903 26.51039 at 30iterations 0.3595072 12.23566 at 40iterations 0.1654780 6.146955 at 50iterations 7.6412186E-02 2.390518 at 60iterations 3.5320386E-02 1.158042 at 70iterations 1.6308954E-02 0.5895729 at 80iterations 7.4950815E-03 0.3089600 at 90iterations 3.4733613E-03 0.1163769 at 100iterations 1.6017099E-03 5.4168224E-02 at 110iterations 7.3854922E-04 2.6675224E-02 at 120iterations finished qdiffx linear iterations at : 11:02:26 total time elapsed so far: 11.55000 # loops : 120 mean,max change (kT/e) : 7.3854922E-04 2.6675224E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 11:02:28 11.734u 0.427s 0:14.22 85.4% 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 11:02:29 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 2.884668 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): -3.919000 35.29600 ymin,ymax (A): -4.302000 48.73500 zmin,zma (A): -24.13700 31.39800 x,y,z range (A): 39.21500 53.03700 55.53500 scale (grids/A): 2.884668 object centre (A): 15.68850 22.21650 3.630500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 290.6260 centred at (gu) : 90.48241 102.5931 90.07862 assigned negative charge : -286.6263 centred at (gu) : 90.74292 103.0657 89.78928 start vw surface at 0.1000000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 138206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 72548 mr = 100936 m= 27124 mr = 60763 m= 6150 mr = 22748 m= 722 mr = 4680 m= 45 mr = 445 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 7888 time to turn everything in is 1.290000 number of dielectric boundary points 55204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 14640 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) : 1.923112 object centre at (A) : 15.68850 22.21650 3.630500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.116704 8.1406347E-02 midg,1,midg; midg,igrid,midg 0.3459591 -4.5697354E-02 1,midg,midg; igrid,midg,midg 1.9335583E-02 -5.9998818E-03 gauss-seidel spectral radius is 0.9992319 estimated iterations to convergence 285 setup time was (sec) 1.610000 now iterating at: 11:02:31 rms-change max change #iterations 8.581459 580.0784 at 10iterations 4.919352 114.1472 at 20iterations 2.800451 58.73900 at 30iterations 1.589513 35.67250 at 40iterations 0.9064642 18.82981 at 50iterations 0.5142545 11.04962 at 60iterations 0.2920791 6.393052 at 70iterations 0.1657744 3.546759 at 80iterations 9.4186716E-02 1.938408 at 90iterations 5.3390425E-02 1.068492 at 100iterations 3.0283395E-02 0.6351624 at 110iterations 1.7169451E-02 0.3681183 at 120iterations 9.7534088E-03 0.1866913 at 130iterations 5.5305976E-03 0.1126413 at 140iterations 3.1368849E-03 6.5922737E-02 at 150iterations 1.7806751E-03 3.8196325E-02 at 160iterations 1.0115388E-03 2.1967173E-02 at 170iterations 5.7494320E-04 1.1088371E-02 at 180iterations finished qdiffx linear iterations at : 11:02:48 total time elapsed so far: 18.80000 # loops : 180 mean,max change (kT/e) : 5.7494320E-04 1.1088371E-02 energy calculations done at 18.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.98000 DelPhi exited at 11:02:49 18.981u 0.458s 0:20.32 95.6% 0+0k 0+0io 0pf+0w