Sun Oct 9 04:35:13 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 Sun Oct 9 2011 at 04:35:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 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: 0.6206848 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): -9.933001 35.99200 ymin,ymax (A): -2.055000 55.30100 zmin,zma (A): -23.95600 27.95900 x,y,z range (A): 45.92500 57.35600 51.91500 scale (grids/A): 0.6206848 object centre (A): 13.02950 26.62300 2.001500 number of atom coordinates read : 2600 total number of charged atoms : 2463 net assigned charge : 8.500016 assigned positive charge : 383.7844 centred at (gu) : 90.04776 90.16695 89.48711 assigned negative charge : -375.2856 centred at (gu) : 90.12724 90.05829 89.49510 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6800 nv = 96 ne = 84 npr = 51626 no. pairs analyzed = 51626 no. exposed pairs = 3578 no. arc points = 25519 no. surface atoms = 1181 nbur = 1419 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 361 mr = 3440 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3000000 number of dielectric boundary points 3683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2443 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8200 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3756655E-09 5.7946683E-09 midg,1,midg; midg,igrid,midg -2.1249481E-10 1.4544582E-08 1,midg,midg; igrid,midg,midg 1.2022906E-08 1.7355509E-09 gauss-seidel spectral radius is 0.9865652 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 04:35:14 rms-change max change #iterations 0.1225421 18.36122 at 10iterations 1.1344848E-02 1.637971 at 20iterations 1.0591992E-03 0.1607437 at 30iterations 1.0005071E-04 1.4869690E-02 at 40iterations 1.1118801E-05 1.5745163E-03 at 50iterations finished qdiffx linear iterations at : 04:35:17 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.1118801E-05 1.5745163E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 04:35:18 4.248u 0.243s 0:04.76 94.1% 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 Sun Oct 9 2011 at 04:35:18 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 = 2600 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: 1.862054 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): -9.933001 35.99200 ymin,ymax (A): -2.055000 55.30100 zmin,zma (A): -23.95600 27.95900 x,y,z range (A): 45.92500 57.35600 51.91500 scale (grids/A): 1.862054 object centre (A): 13.02950 26.62300 2.001500 number of atom coordinates read : 2600 total number of charged atoms : 2463 net assigned charge : 8.500016 assigned positive charge : 383.7844 centred at (gu) : 90.14255 90.50004 88.46031 assigned negative charge : -375.2856 centred at (gu) : 90.38153 90.17471 88.48486 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72059 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25519 grid for indexing accessible points = 1.400000 m= 25433 mr = 47606 m= 3838 mr = 17930 m= 196 mr = 2107 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 311 time to turn everything in is 0.5600000 number of dielectric boundary points 33819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19292 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) : 0.6206848 object centre at (A) : 13.02950 26.62300 2.001500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4985840E-02 2.4510780E-03 midg,1,midg; midg,igrid,midg 3.2695243E-03 3.1460214E-02 1,midg,midg; igrid,midg,midg 2.1251252E-02 6.1887745E-03 gauss-seidel spectral radius is 0.9985862 estimated iterations to convergence 211 setup time was (sec) 0.9000000 now iterating at: 04:35:19 rms-change max change #iterations 3.967082 178.8511 at 10iterations 1.821911 63.70021 at 20iterations 0.8402676 25.75264 at 30iterations 0.3878177 12.09224 at 40iterations 0.1782121 6.238674 at 50iterations 8.2437687E-02 3.261891 at 60iterations 3.8021024E-02 1.296989 at 70iterations 1.7533496E-02 0.5433311 at 80iterations 8.1124781E-03 0.2807267 at 90iterations 3.7421118E-03 0.1195555 at 100iterations 1.7391565E-03 6.0680389E-02 at 110iterations 8.0278108E-04 2.4374008E-02 at 120iterations finished qdiffx linear iterations at : 04:35:28 total time elapsed so far: 9.770000 # loops : 120 mean,max change (kT/e) : 8.0278108E-04 2.4374008E-02 energy calculations done at 9.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.950000 DelPhi exited at 04:35:29 9.950u 0.332s 0:10.57 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 Sun Oct 9 2011 at 04:35:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 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: 2.793082 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): -9.933001 35.99200 ymin,ymax (A): -2.055000 55.30100 zmin,zma (A): -23.95600 27.95900 x,y,z range (A): 45.92500 57.35600 51.91500 scale (grids/A): 2.793082 object centre (A): 13.02950 26.62300 2.001500 number of atom coordinates read : 2600 total number of charged atoms : 2463 net assigned charge : 8.500016 assigned positive charge : 383.7844 centred at (gu) : 90.21356 90.74976 87.69032 assigned negative charge : -375.2856 centred at (gu) : 90.57224 90.26204 87.72734 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 166430 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25519 grid for indexing accessible points = 1.400000 m= 82312 mr = 116169 m= 29360 mr = 65259 m= 6561 mr = 22691 m= 823 mr = 4507 m= 49 mr = 495 m= 0 mr = 13 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 1081 time to turn everything in is 1.470000 number of dielectric boundary points 76401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 19701 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) : 1.862054 object centre at (A) : 13.02950 26.62300 2.001500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4955728 6.9719158E-02 midg,1,midg; midg,igrid,midg -4.3502688E-02 0.4332230 1,midg,midg; igrid,midg,midg 0.2478775 7.2013557E-02 gauss-seidel spectral radius is 0.9992534 estimated iterations to convergence 289 setup time was (sec) 1.830000 now iterating at: 04:35:31 rms-change max change #iterations 9.525413 295.5446 at 10iterations 5.592058 159.7299 at 20iterations 3.260783 75.28096 at 30iterations 1.889886 69.28099 at 40iterations 1.095194 22.35660 at 50iterations 0.6323519 14.60472 at 60iterations 0.3644000 7.138876 at 70iterations 0.2095576 4.723898 at 80iterations 0.1206381 2.240932 at 90iterations 6.9281220E-02 1.458035 at 100iterations 3.9741151E-02 0.7827682 at 110iterations 2.2823779E-02 0.5933390 at 120iterations 1.3104427E-02 0.2718832 at 130iterations 7.5046020E-03 0.1481647 at 140iterations 4.3074158E-03 7.9311371E-02 at 150iterations 2.4675808E-03 4.6287537E-02 at 160iterations 1.4177448E-03 2.8162003E-02 at 170iterations 8.1321085E-04 1.7143250E-02 at 180iterations finished qdiffx linear iterations at : 04:35:45 total time elapsed so far: 16.03000 # loops : 180 mean,max change (kT/e) : 8.1321085E-04 1.7143250E-02 energy calculations done at 16.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.22000 DelPhi exited at 04:35:45 16.220u 0.315s 0:16.80 98.3% 0+0k 0+0io 0pf+0w