Sun Oct 9 14:16:22 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 14:16:22 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 = 2658 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: 0.5584401 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): -1.427000 49.28200 ymin,ymax (A): -7.948000 39.40000 zmin,zma (A): -16.05200 47.69700 x,y,z range (A): 50.70900 47.34800 63.74900 scale (grids/A): 0.5584401 object centre (A): 23.92750 15.72600 15.82250 number of atom coordinates read : 2658 total number of charged atoms : 2519 net assigned charge : 7.000018 assigned positive charge : 400.5884 centred at (gu) : 90.15797 90.25376 89.35677 assigned negative charge : -393.5895 centred at (gu) : 90.11996 90.14201 89.37152 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5447 nv = 96 ne = 84 npr = 52324 no. pairs analyzed = 52324 no. exposed pairs = 3428 no. arc points = 24201 no. surface atoms = 1154 nbur = 1504 mkacc time = 0.1100000 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 = 1.540000 m= 226 mr = 2774 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2458 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7018 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7323405E-10 4.8378518E-10 midg,1,midg; midg,igrid,midg -3.2991057E-10 1.8309296E-09 1,midg,midg; igrid,midg,midg 3.3204370E-10 1.0902260E-09 gauss-seidel spectral radius is 0.9834362 estimated iterations to convergence 64 setup time was (sec) 0.5000000 now iterating at: 14:16:23 rms-change max change #iterations 7.6616786E-02 15.38118 at 10iterations 5.3330767E-03 0.9614296 at 20iterations 4.1431159E-04 6.8107605E-02 at 30iterations 5.1384257E-05 1.0860443E-02 at 40iterations 1.1308702E-05 2.5424957E-03 at 50iterations finished qdiffx linear iterations at : 14:16:25 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.1308702E-05 2.5424957E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 14:16:25 3.088u 0.149s 0:03.51 91.7% 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 14:16:25 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 = 2658 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: 1.675320 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): -1.427000 49.28200 ymin,ymax (A): -7.948000 39.40000 zmin,zma (A): -16.05200 47.69700 x,y,z range (A): 50.70900 47.34800 63.74900 scale (grids/A): 1.675320 object centre (A): 23.92750 15.72600 15.82250 number of atom coordinates read : 2658 total number of charged atoms : 2519 net assigned charge : 7.000018 assigned positive charge : 400.5884 centred at (gu) : 90.47315 90.76048 88.06959 assigned negative charge : -393.5895 centred at (gu) : 90.35966 90.42600 88.11437 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 60331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24201 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18212 mr = 40621 m= 1810 mr = 12105 m= 68 mr = 765 m= 0 mr = 6 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 26924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 19402 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) : 0.5584401 object centre at (A) : 23.92750 15.72600 15.82250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1727718E-02 1.2050899E-02 midg,1,midg; midg,igrid,midg 4.7151771E-05 4.2284378E-03 1,midg,midg; igrid,midg,midg -7.1709990E-03 3.9733322E-03 gauss-seidel spectral radius is 0.9982532 estimated iterations to convergence 190 setup time was (sec) 0.6800000 now iterating at: 14:16:26 rms-change max change #iterations 3.256646 178.3436 at 10iterations 1.385937 53.46062 at 20iterations 0.5839236 22.20320 at 30iterations 0.2489328 9.250267 at 40iterations 0.1050597 4.101952 at 50iterations 4.4576190E-02 1.662407 at 60iterations 1.8904790E-02 0.7262936 at 70iterations 8.0278115E-03 0.3274641 at 80iterations 3.4101771E-03 0.1351986 at 90iterations 1.4477943E-03 5.2075624E-02 at 100iterations 6.1749213E-04 2.6884079E-02 at 110iterations 2.6391048E-04 1.0242462E-02 at 120iterations finished qdiffx linear iterations at : 14:16:32 total time elapsed so far: 6.560000 # loops : 120 mean,max change (kT/e) : 2.6391048E-04 1.0242462E-02 energy calculations done at 6.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.740000 DelPhi exited at 14:16:33 6.743u 0.147s 0:07.15 96.2% 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 14:16:33 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 = 2658 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: 2.512980 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): -1.427000 49.28200 ymin,ymax (A): -7.948000 39.40000 zmin,zma (A): -16.05200 47.69700 x,y,z range (A): 50.70900 47.34800 63.74900 scale (grids/A): 2.512980 object centre (A): 23.92750 15.72600 15.82250 number of atom coordinates read : 2658 total number of charged atoms : 2519 net assigned charge : 7.000018 assigned positive charge : 400.5884 centred at (gu) : 90.70960 91.14057 87.10440 assigned negative charge : -393.5895 centred at (gu) : 90.53956 90.63888 87.17148 start vw surface at 0.1500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 139989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24201 grid for indexing accessible points = 1.400000 m= 63254 mr = 99413 m= 17365 mr = 49283 m= 2749 mr = 12507 m= 240 mr = 1649 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 60661 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 20121 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) : 1.675320 object centre at (A) : 23.92750 15.72600 15.82250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7979296 0.2104749 midg,1,midg; midg,igrid,midg 1.4989468E-03 1.1589988E-02 1,midg,midg; igrid,midg,midg -8.6729437E-02 4.7786180E-02 gauss-seidel spectral radius is 0.9991534 estimated iterations to convergence 271 setup time was (sec) 1.340000 now iterating at: 14:16:34 rms-change max change #iterations 8.489059 282.6505 at 10iterations 4.839235 150.8878 at 20iterations 2.751804 65.65411 at 30iterations 1.548876 38.34571 at 40iterations 0.8682123 21.83135 at 50iterations 0.4861497 11.16203 at 60iterations 0.2713867 5.583321 at 70iterations 0.1508048 3.588213 at 80iterations 8.3847754E-02 1.812145 at 90iterations 4.6558961E-02 1.124252 at 100iterations 2.5827443E-02 0.6142378 at 110iterations 1.4287472E-02 0.2991238 at 120iterations 7.9367924E-03 0.1754868 at 130iterations 4.3879347E-03 0.1006317 at 140iterations 2.4330374E-03 5.4210663E-02 at 150iterations 1.3469928E-03 2.7875900E-02 at 160iterations 7.4704638E-04 1.5779495E-02 at 170iterations 4.1682212E-04 8.5706711E-03 at 180iterations finished qdiffx linear iterations at : 14:16:44 total time elapsed so far: 11.43000 # loops : 180 mean,max change (kT/e) : 4.1682212E-04 8.5706711E-03 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 14:16:45 11.605u 0.196s 0:12.18 96.7% 0+0k 0+0io 0pf+0w