Mon Oct 10 13:54:37 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 Mon Oct 10 2011 at 13:54:37 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 = 1064 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7490321 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): -27.45200 10.37400 ymin,ymax (A): 1.420000 41.45000 zmin,zma (A): 10.83800 58.36600 x,y,z range (A): 37.82600 40.03000 47.52800 scale (grids/A): 0.7490321 object centre (A): -8.539000 21.43500 34.60200 number of atom coordinates read : 1064 total number of charged atoms : 938 net assigned charge : 1.500003 assigned positive charge : 148.2851 centred at (gu) : 91.76942 91.49309 91.76160 assigned negative charge : -146.7850 centred at (gu) : 91.59391 91.61449 91.47180 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4245 nv = 96 ne = 84 npr = 21378 no. pairs analyzed = 21378 no. exposed pairs = 1657 no. arc points = 12238 no. surface atoms = 553 nbur = 511 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 1921 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 2598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 954 ## 65 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.7915134E-08 2.5800259E-07 midg,1,midg; midg,igrid,midg 7.2041061E-08 -5.3918669E-08 1,midg,midg; igrid,midg,midg -5.0272881E-08 1.7322888E-07 gauss-seidel spectral radius is 0.9906101 estimated iterations to convergence 84 setup time was (sec) 0.3100000 now iterating at: 13:54:38 rms-change max change #iterations 0.1684134 26.90300 at 10iterations 2.2423459E-02 4.549507 at 20iterations 3.0471620E-03 0.5631104 at 30iterations 4.1746409E-04 6.5547228E-02 at 40iterations 5.4977532E-05 1.0308266E-02 at 50iterations finished qdiffx linear iterations at : 13:54:41 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 5.4977532E-05 1.0308266E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 13:54:41 3.360u 0.158s 0:04.10 85.6% 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 13:54:41 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 = 1064 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.247097 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): -27.45200 10.37400 ymin,ymax (A): 1.420000 41.45000 zmin,zma (A): 10.83800 58.36600 x,y,z range (A): 37.82600 40.03000 47.52800 scale (grids/A): 2.247097 object centre (A): -8.539000 21.43500 34.60200 number of atom coordinates read : 1064 total number of charged atoms : 938 net assigned charge : 1.500003 assigned positive charge : 148.2851 centred at (gu) : 95.30837 94.47936 95.28494 assigned negative charge : -146.7850 centred at (gu) : 94.78176 94.84344 94.41534 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 43149 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12238 grid for indexing accessible points = 1.400000 m= 16725 mr = 25905 m= 3864 mr = 11739 m= 443 mr = 2466 m= 11 mr = 179 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 23903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 7481 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) : 0.7490321 object centre at (A) : -8.539000 21.43500 34.60200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0597946E-03 5.4268751E-02 midg,1,midg; midg,igrid,midg 2.0957017E-02 6.0071214E-03 1,midg,midg; igrid,midg,midg -1.0559581E-02 2.5155768E-03 gauss-seidel spectral radius is 0.9988562 estimated iterations to convergence 234 setup time was (sec) 0.4700000 now iterating at: 13:54:42 rms-change max change #iterations 3.431604 244.0578 at 10iterations 1.699631 80.22314 at 20iterations 0.8455744 35.36403 at 30iterations 0.4189289 17.25081 at 40iterations 0.2085701 8.342615 at 50iterations 0.1041674 4.318310 at 60iterations 5.1629074E-02 1.969376 at 70iterations 2.5543222E-02 0.9526768 at 80iterations 1.2702262E-02 0.5078964 at 90iterations 6.3184807E-03 0.2429991 at 100iterations 3.1556210E-03 0.1237683 at 110iterations 1.5581208E-03 6.0966969E-02 at 120iterations finished qdiffx linear iterations at : 13:54:49 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.5581208E-03 6.0966969E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 13:54:50 7.682u 0.207s 0:08.46 93.1% 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 Mon Oct 10 2011 at 13:54:50 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 = 1064 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.370645 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): -27.45200 10.37400 ymin,ymax (A): 1.420000 41.45000 zmin,zma (A): 10.83800 58.36600 x,y,z range (A): 37.82600 40.03000 47.52800 scale (grids/A): 3.370645 object centre (A): -8.539000 21.43500 34.60200 number of atom coordinates read : 1064 total number of charged atoms : 938 net assigned charge : 1.500003 assigned positive charge : 148.2851 centred at (gu) : 97.96252 96.71907 97.92745 assigned negative charge : -146.7850 centred at (gu) : 97.17265 97.26516 96.62305 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 98965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12238 grid for indexing accessible points = 1.400000 m= 49628 mr = 63267 m= 22302 mr = 38602 m= 7417 mr = 17708 m= 1668 mr = 5574 m= 214 mr = 1080 m= 13 mr = 128 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 53848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 7504 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) : 2.247097 object centre at (A) : -8.539000 21.43500 34.60200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0496167E-02 0.4854507 midg,1,midg; midg,igrid,midg 0.1655770 3.9737720E-02 1,midg,midg; igrid,midg,midg -4.5361716E-02 -2.2860192E-02 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 0.9500000 now iterating at: 13:54:51 rms-change max change #iterations 7.644594 323.0745 at 10iterations 4.506345 135.2497 at 20iterations 2.666079 76.92514 at 30iterations 1.568766 42.24184 at 40iterations 0.9222469 23.67593 at 50iterations 0.5404748 12.89543 at 60iterations 0.3148759 8.064728 at 70iterations 0.1840167 5.049726 at 80iterations 0.1075630 2.540925 at 90iterations 6.2876664E-02 1.408052 at 100iterations 3.6746446E-02 0.8663278 at 110iterations 2.1389307E-02 0.4510040 at 120iterations 1.2491672E-02 0.2998896 at 130iterations 7.2730347E-03 0.1624947 at 140iterations 4.2478885E-03 9.9395752E-02 at 150iterations 2.4743229E-03 5.3073823E-02 at 160iterations 1.4444544E-03 3.6436558E-02 at 170iterations 8.4405468E-04 1.8315315E-02 at 180iterations finished qdiffx linear iterations at : 13:55:02 total time elapsed so far: 11.96000 # loops : 180 mean,max change (kT/e) : 8.4405468E-04 1.8315315E-02 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 13:55:03 12.089u 0.236s 0:12.96 94.9% 0+0k 0+0io 0pf+0w