Sat Oct 8 17:47:37 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+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 Sat Oct 8 2011 at 17:47:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3353 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: 0.5314226 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): -11.18000 42.66000 ymin,ymax (A): -38.47400 28.51600 zmin,zma (A): -15.40800 34.39600 x,y,z range (A): 53.84000 66.99001 49.80400 scale (grids/A): 0.5314226 object centre (A): 15.74000 -4.979002 9.493999 number of atom coordinates read : 3353 total number of charged atoms : 3208 net assigned charge : -1.999991 assigned positive charge : 501.8016 centred at (gu) : 90.01774 91.41987 90.32147 assigned negative charge : -503.8029 centred at (gu) : 90.05318 91.37447 90.28783 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6110 nv = 96 ne = 84 npr = 67411 no. pairs analyzed = 67411 no. exposed pairs = 4130 no. arc points = 28505 no. surface atoms = 1395 nbur = 1958 mkacc time = 0.2300000 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 = 1.624000 m= 238 mr = 3280 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 3055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2845 ## 383 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 8044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0088593E-10 7.7637209E-11 midg,1,midg; midg,igrid,midg -1.8783998E-10 1.7707912E-10 1,midg,midg; igrid,midg,midg 7.8483678E-11 -2.2680340E-10 gauss-seidel spectral radius is 0.9817793 estimated iterations to convergence 61 setup time was (sec) 0.7500000 now iterating at: 17:47:38 rms-change max change #iterations 6.8077184E-02 12.75066 at 10iterations 4.1775983E-03 0.6118641 at 20iterations 3.1101931E-04 5.0859451E-02 at 30iterations 4.5407920E-05 6.4883232E-03 at 40iterations 1.2155556E-05 1.6689301E-03 at 50iterations finished qdiffx linear iterations at : 17:47:42 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 1.2155556E-05 1.6689301E-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) 4.610000 DelPhi exited at 17:47:43 4.614u 0.416s 0:05.32 94.3% 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 17:47:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3353 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: 1.594268 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): -11.18000 42.66000 ymin,ymax (A): -38.47400 28.51600 zmin,zma (A): -15.40800 34.39600 x,y,z range (A): 53.84000 66.99001 49.80400 scale (grids/A): 1.594268 object centre (A): 15.74000 -4.979002 9.493999 number of atom coordinates read : 3353 total number of charged atoms : 3208 net assigned charge : -1.999991 assigned positive charge : 501.8016 centred at (gu) : 90.05219 94.25893 90.96327 assigned negative charge : -503.8029 centred at (gu) : 90.15936 94.12285 90.86312 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 68539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28505 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21447 mr = 47759 m= 1929 mr = 14896 m= 44 mr = 876 m= 0 mr = 2 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 183 time to turn everything in is 0.7300000 number of dielectric boundary points 28426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 342 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 24440 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) : 0.5314226 object centre at (A) : 15.74000 -4.979002 9.493999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8662309E-03 2.0160705E-03 midg,1,midg; midg,igrid,midg 7.0887338E-03 3.8714181E-03 1,midg,midg; igrid,midg,midg 1.2012150E-03 -7.0080962E-03 gauss-seidel spectral radius is 0.9981227 estimated iterations to convergence 183 setup time was (sec) 1.060000 now iterating at: 17:47:44 rms-change max change #iterations 3.346355 145.5981 at 10iterations 1.373226 61.51246 at 20iterations 0.5635939 20.95684 at 30iterations 0.2322748 8.569452 at 40iterations 9.5404282E-02 3.461555 at 50iterations 3.9384596E-02 1.451824 at 60iterations 1.6161699E-02 0.6233597 at 70iterations 6.6767130E-03 0.2439041 at 80iterations 2.7525558E-03 9.9205017E-02 at 90iterations 1.1417572E-03 3.8196564E-02 at 100iterations 4.7679245E-04 1.7114639E-02 at 110iterations 2.0465198E-04 7.3242188E-03 at 120iterations finished qdiffx linear iterations at : 17:47:54 total time elapsed so far: 10.63000 # loops : 120 mean,max change (kT/e) : 2.0465198E-04 7.3242188E-03 energy calculations done at 10.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.83000 DelPhi exited at 17:47:54 10.838u 0.488s 0:11.60 97.5% 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 17:47:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3353 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: 2.391402 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): -11.18000 42.66000 ymin,ymax (A): -38.47400 28.51600 zmin,zma (A): -15.40800 34.39600 x,y,z range (A): 53.84000 66.99001 49.80400 scale (grids/A): 2.391402 object centre (A): 15.74000 -4.979002 9.493999 number of atom coordinates read : 3353 total number of charged atoms : 3208 net assigned charge : -1.999991 assigned positive charge : 501.8016 centred at (gu) : 90.07804 96.38803 91.44495 assigned negative charge : -503.8029 centred at (gu) : 90.23911 96.18420 91.29450 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 159424 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28505 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 75324 mr = 116669 m= 20499 mr = 60237 m= 3032 mr = 15361 m= 188 mr = 1885 m= 4 mr = 64 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 618 time to turn everything in is 1.740000 number of dielectric boundary points 64256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 25618 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) : 1.594268 object centre at (A) : 15.74000 -4.979002 9.493999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1059042 4.8370034E-02 midg,1,midg; midg,igrid,midg 0.1479837 0.1222871 1,midg,midg; igrid,midg,midg 2.1904651E-02 -8.7896556E-02 gauss-seidel spectral radius is 0.9991232 estimated iterations to convergence 267 setup time was (sec) 2.100000 now iterating at: 17:47:57 rms-change max change #iterations 8.790599 310.5387 at 10iterations 4.926703 111.7281 at 20iterations 2.738256 63.23490 at 30iterations 1.516418 35.49138 at 40iterations 0.8378546 16.72723 at 50iterations 0.4624168 10.43281 at 60iterations 0.2540649 5.292915 at 70iterations 0.1395464 2.714911 at 80iterations 7.6513298E-02 1.691413 at 90iterations 4.2019438E-02 0.8375096 at 100iterations 2.3030419E-02 0.4754926 at 110iterations 1.2615440E-02 0.2461929 at 120iterations 6.9113001E-03 0.1415325 at 130iterations 3.7909569E-03 7.1662903E-02 at 140iterations 2.0843600E-03 4.1584015E-02 at 150iterations 1.1521836E-03 2.7482986E-02 at 160iterations 6.4016040E-04 1.4040947E-02 at 170iterations 3.6086226E-04 8.4304810E-03 at 180iterations finished qdiffx linear iterations at : 17:48:12 total time elapsed so far: 16.89000 # loops : 180 mean,max change (kT/e) : 3.6086226E-04 8.4304810E-03 energy calculations done at 16.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.10000 DelPhi exited at 17:48:12 17.100u 0.500s 0:17.89 98.3% 0+0k 0+0io 0pf+0w