Mon Oct 10 14:15:55 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 14:15:55 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3853 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: 0.5110023 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): -38.32700 27.55700 ymin,ymax (A): -23.15200 46.51500 zmin,zma (A): -77.02400 -7.667000 x,y,z range (A): 65.88400 69.66701 69.35700 scale (grids/A): 0.5110023 object centre (A): -5.385000 11.68150 -42.34550 number of atom coordinates read : 3853 total number of charged atoms : 3684 net assigned charge : -9.999972 assigned positive charge : 579.1396 centred at (gu) : 90.43966 86.96931 90.84943 assigned negative charge : -589.1420 centred at (gu) : 90.50060 86.87074 90.87840 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6620 nv = 96 ne = 84 npr = 72904 no. pairs analyzed = 72904 no. exposed pairs = 5732 no. arc points = 41569 no. surface atoms = 1892 nbur = 1961 mkacc time = 0.1900000 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 = 1.680000 m= 226 mr = 2844 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4004 ## 619 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8803 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8646886E-11 -2.4487395E-10 midg,1,midg; midg,igrid,midg -7.8357298E-10 3.1490713E-11 1,midg,midg; igrid,midg,midg -4.5165109E-12 -2.9813499E-10 gauss-seidel spectral radius is 0.9803733 estimated iterations to convergence 59 setup time was (sec) 0.7000000 now iterating at: 14:15:56 rms-change max change #iterations 5.8733653E-02 10.47291 at 10iterations 3.2388226E-03 0.5762539 at 20iterations 1.8970076E-04 3.1147003E-02 at 30iterations 1.4069126E-05 2.4719238E-03 at 40iterations 2.1436465E-06 4.5919418E-04 at 50iterations finished qdiffx linear iterations at : 14:16:00 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 2.1436465E-06 4.5919418E-04 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 14:16:01 4.622u 0.414s 0:06.18 81.3% 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 14:16:01 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3853 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: 1.533007 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): -38.32700 27.55700 ymin,ymax (A): -23.15200 46.51500 zmin,zma (A): -77.02400 -7.667000 x,y,z range (A): 65.88400 69.66701 69.35700 scale (grids/A): 1.533007 object centre (A): -5.385000 11.68150 -42.34550 number of atom coordinates read : 3853 total number of charged atoms : 3684 net assigned charge : -9.999972 assigned positive charge : 579.1396 centred at (gu) : 91.31773 80.90704 92.54737 assigned negative charge : -589.1420 centred at (gu) : 91.50150 80.61189 92.63494 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 73395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41569 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 19225 mr = 44662 m= 1544 mr = 11478 m= 36 mr = 496 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.6400000 number of dielectric boundary points 37565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 554 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 27669 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) : 0.5110023 object centre at (A) : -5.385000 11.68150 -42.34550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1239933E-02 -7.6963827E-03 midg,1,midg; midg,igrid,midg -1.4849246E-02 2.2029763E-03 1,midg,midg; igrid,midg,midg -2.2395477E-03 -5.2327216E-03 gauss-seidel spectral radius is 0.9980388 estimated iterations to convergence 180 setup time was (sec) 0.9800000 now iterating at: 14:16:03 rms-change max change #iterations 3.347907 149.6140 at 10iterations 1.334750 50.26197 at 20iterations 0.5340587 20.74106 at 30iterations 0.2140830 7.993045 at 40iterations 8.5830167E-02 3.159018 at 50iterations 3.4546461E-02 1.237322 at 60iterations 1.3874597E-02 0.4969101 at 70iterations 5.5728243E-03 0.2064753 at 80iterations 2.2469740E-03 8.6170197E-02 at 90iterations 9.0272335E-04 3.0244827E-02 at 100iterations 3.6160310E-04 1.2741089E-02 at 110iterations 1.4655299E-04 5.2633286E-03 at 120iterations finished qdiffx linear iterations at : 14:16:12 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 1.4655299E-04 5.2633286E-03 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.55000 DelPhi exited at 14:16:13 10.557u 0.451s 0:11.35 96.9% 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 14:16:13 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3853 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: 2.299510 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): -38.32700 27.55700 ymin,ymax (A): -23.15200 46.51500 zmin,zma (A): -77.02400 -7.667000 x,y,z range (A): 65.88400 69.66701 69.35700 scale (grids/A): 2.299510 object centre (A): -5.385000 11.68150 -42.34550 number of atom coordinates read : 3853 total number of charged atoms : 3684 net assigned charge : -9.999972 assigned positive charge : 579.1396 centred at (gu) : 91.97636 76.36028 93.82085 assigned negative charge : -589.1420 centred at (gu) : 92.25224 75.91782 93.95238 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 170527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41569 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 68931 mr = 111377 m= 16376 mr = 50112 m= 2056 mr = 10690 m= 105 mr = 1010 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 511 time to turn everything in is 1.500000 number of dielectric boundary points 84784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 29396 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) : 1.533007 object centre at (A) : -5.385000 11.68150 -42.34550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2132069 -0.1188726 midg,1,midg; midg,igrid,midg -9.6654862E-02 6.4259544E-02 1,midg,midg; igrid,midg,midg -6.0524337E-02 -8.2004443E-02 gauss-seidel spectral radius is 0.9991106 estimated iterations to convergence 265 setup time was (sec) 1.830000 now iterating at: 14:16:15 rms-change max change #iterations 9.266804 285.3205 at 10iterations 5.238146 140.4166 at 20iterations 2.935148 68.84615 at 30iterations 1.629530 36.31693 at 40iterations 0.8996129 20.02147 at 50iterations 0.4968052 10.71572 at 60iterations 0.2738633 5.828475 at 70iterations 0.1499163 3.182812 at 80iterations 8.1985071E-02 1.679748 at 90iterations 4.4805408E-02 0.9621801 at 100iterations 2.4505900E-02 0.5229721 at 110iterations 1.3352953E-02 0.3116398 at 120iterations 7.2972798E-03 0.1527338 at 130iterations 3.9681792E-03 7.9339981E-02 at 140iterations 2.1644193E-03 4.8015833E-02 at 150iterations 1.1781974E-03 2.4429560E-02 at 160iterations 6.4264436E-04 1.3224602E-02 at 170iterations 3.4969600E-04 7.0137978E-03 at 180iterations finished qdiffx linear iterations at : 14:16:31 total time elapsed so far: 17.84000 # loops : 180 mean,max change (kT/e) : 3.4969600E-04 7.0137978E-03 energy calculations done at 17.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.01000 DelPhi exited at 14:16:32 18.017u 0.484s 0:18.93 97.6% 0+0k 0+0io 0pf+0w