Tue Oct 11 05:49:53 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 Tue Oct 11 2011 at 05:49:53 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7311262 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): 25.61200 72.11700 ymin,ymax (A): -18.78000 29.91200 zmin,zma (A): 3.938000 46.39400 x,y,z range (A): 46.50500 48.69200 42.45600 scale (grids/A): 0.7311262 object centre (A): 48.86450 5.566001 25.16600 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 89.19659 90.60574 90.26426 assigned negative charge : -312.6442 centred at (gu) : 89.33153 90.55222 90.34970 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7811 nv = 96 ne = 84 npr = 41679 no. pairs analyzed = 41679 no. exposed pairs = 2579 no. arc points = 17597 no. surface atoms = 883 nbur = 1407 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 547 mr = 4576 m= 8 mr = 108 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 0.2600000 number of dielectric boundary points 3682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1536 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5540893E-07 2.2973209E-08 midg,1,midg; midg,igrid,midg 4.4052676E-08 1.5368472E-07 1,midg,midg; igrid,midg,midg 2.3670457E-07 -1.6035084E-08 gauss-seidel spectral radius is 0.9902452 estimated iterations to convergence 82 setup time was (sec) 0.5000000 now iterating at: 05:49:53 rms-change max change #iterations 0.2280781 33.95981 at 10iterations 3.0392397E-02 3.958700 at 20iterations 4.2969887E-03 0.5397873 at 30iterations 7.8071718E-04 9.2446327E-02 at 40iterations 2.1612276E-04 2.3477554E-02 at 50iterations finished qdiffx linear iterations at : 05:49:56 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 2.1612276E-04 2.3477554E-02 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 05:49:57 3.243u 0.170s 0:04.26 80.0% 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 Tue Oct 11 2011 at 05:49:57 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.193379 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): 25.61200 72.11700 ymin,ymax (A): -18.78000 29.91200 zmin,zma (A): 3.938000 46.39400 x,y,z range (A): 46.50500 48.69200 42.45600 scale (grids/A): 2.193379 object centre (A): 48.86450 5.566001 25.16600 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 87.59010 91.81731 90.79267 assigned negative charge : -312.6442 centred at (gu) : 87.99464 91.65670 91.04937 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17597 grid for indexing accessible points = 1.400000 m= 34833 mr = 58754 m= 7334 mr = 26778 m= 777 mr = 5022 m= 30 mr = 417 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 33800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15649 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) : 0.7311262 object centre at (A) : 48.86450 5.566001 25.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7221529E-02 3.1078555E-02 midg,1,midg; midg,igrid,midg 4.9140029E-02 3.2982625E-02 1,midg,midg; igrid,midg,midg 5.1917031E-02 -5.5003196E-02 gauss-seidel spectral radius is 0.9988986 estimated iterations to convergence 238 setup time was (sec) 0.8900000 now iterating at: 05:49:58 rms-change max change #iterations 4.902229 198.0233 at 10iterations 2.476240 99.03352 at 20iterations 1.254378 34.91207 at 30iterations 0.6349269 19.60812 at 40iterations 0.3217179 8.847073 at 50iterations 0.1634220 4.525293 at 60iterations 8.3058015E-02 2.349551 at 70iterations 4.2264376E-02 1.199987 at 80iterations 2.1482680E-02 0.5732269 at 90iterations 1.1072324E-02 0.3726082 at 100iterations 5.7276525E-03 0.1746693 at 110iterations 3.0609372E-03 9.2346191E-02 at 120iterations finished qdiffx linear iterations at : 05:50:05 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 3.0609372E-03 9.2346191E-02 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 05:50:06 8.272u 0.227s 0:08.93 95.0% 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 Tue Oct 11 2011 at 05:50:06 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.290068 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): 25.61200 72.11700 ymin,ymax (A): -18.78000 29.91200 zmin,zma (A): 3.938000 46.39400 x,y,z range (A): 46.50500 48.69200 42.45600 scale (grids/A): 3.290068 object centre (A): 48.86450 5.566001 25.16600 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 86.38500 92.72600 91.18912 assigned negative charge : -312.6442 centred at (gu) : 86.99200 92.48519 91.57398 start vw surface at 0.1500000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 188054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17597 grid for indexing accessible points = 1.400000 m= 106204 mr = 140726 m= 46215 mr = 89311 m= 14185 mr = 38474 m= 3085 mr = 11063 m= 371 mr = 2246 m= 16 mr = 226 m= 0 mr = 9 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.930000 number of dielectric boundary points 76075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 15748 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) : 2.193379 object centre at (A) : 48.86450 5.566001 25.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1276586 0.2641968 midg,1,midg; midg,igrid,midg 0.3733091 0.1794632 1,midg,midg; igrid,midg,midg 0.4849937 -0.6555195 gauss-seidel spectral radius is 0.9993153 estimated iterations to convergence 301 setup time was (sec) 2.240000 now iterating at: 05:50:09 rms-change max change #iterations 10.77526 388.8745 at 10iterations 6.436143 135.2716 at 20iterations 3.832512 76.56679 at 30iterations 2.282463 41.23864 at 40iterations 1.355188 26.81650 at 50iterations 0.8021953 14.34280 at 60iterations 0.4755109 9.628368 at 70iterations 0.2812943 5.012661 at 80iterations 0.1662847 2.725887 at 90iterations 9.8209642E-02 1.680299 at 100iterations 5.8144782E-02 1.033514 at 110iterations 3.4546494E-02 0.5809813 at 120iterations 2.0604953E-02 0.3333306 at 130iterations 1.2442848E-02 0.2561607 at 140iterations 7.6954416E-03 0.1379242 at 150iterations 4.9238228E-03 8.2309723E-02 at 160iterations 3.3383374E-03 6.3415527E-02 at 170iterations 2.4110714E-03 4.4010162E-02 at 180iterations finished qdiffx linear iterations at : 05:50:20 total time elapsed so far: 13.70000 # loops : 180 mean,max change (kT/e) : 2.4110714E-03 4.4010162E-02 energy calculations done at 13.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.87000 DelPhi exited at 05:50:21 13.871u 0.234s 0:14.75 95.5% 0+0k 0+0io 0pf+0w