Sun Oct 9 11:40:26 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 11:40:26 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 = 3113 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5341336 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): -16.75100 49.89900 ymin,ymax (A): -24.18900 27.22900 zmin,zma (A): -19.13400 43.12700 x,y,z range (A): 66.64999 51.41800 62.26100 scale (grids/A): 0.5341336 object centre (A): 16.57400 1.520000 11.99650 number of atom coordinates read : 3113 total number of charged atoms : 3044 net assigned charge : -2.499987 assigned positive charge : 467.1192 centred at (gu) : 91.46536 90.60165 90.10695 assigned negative charge : -469.6212 centred at (gu) : 91.30431 90.67464 90.13372 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6191 nv = 96 ne = 84 npr = 56590 no. pairs analyzed = 56590 no. exposed pairs = 4669 no. arc points = 34716 no. surface atoms = 1540 nbur = 1573 mkacc time = 0.1000000 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 = 1.596000 m= 257 mr = 2708 m= 0 mr = 7 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3362 ## 389 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7985 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2950259E-11 -2.3122006E-10 midg,1,midg; midg,igrid,midg 1.8518687E-10 -5.0559629E-10 1,midg,midg; igrid,midg,midg -5.7785154E-10 8.7545277E-10 gauss-seidel spectral radius is 0.9819779 estimated iterations to convergence 61 setup time was (sec) 0.4000000 now iterating at: 11:40:27 rms-change max change #iterations 6.5379970E-02 13.81641 at 10iterations 4.0761624E-03 0.7752228 at 20iterations 2.6002893E-04 4.4459343E-02 at 30iterations 2.0565918E-05 2.9897690E-03 at 40iterations 2.4140902E-06 3.3664703E-04 at 50iterations finished qdiffx linear iterations at : 11:40:30 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.4140902E-06 3.3664703E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 11:40:30 3.388u 0.161s 0:03.83 92.4% 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 11:40:30 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 = 3113 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.602401 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): -16.75100 49.89900 ymin,ymax (A): -24.18900 27.22900 zmin,zma (A): -19.13400 43.12700 x,y,z range (A): 66.64999 51.41800 62.26100 scale (grids/A): 1.602401 object centre (A): 16.57400 1.520000 11.99650 number of atom coordinates read : 3113 total number of charged atoms : 3044 net assigned charge : -2.499987 assigned positive charge : 467.1192 centred at (gu) : 94.39500 91.80376 90.31997 assigned negative charge : -469.6212 centred at (gu) : 93.91246 92.02361 90.40099 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67423 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34716 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19784 mr = 41363 m= 2186 mr = 12504 m= 54 mr = 1001 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 34580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 23217 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) : 0.5341336 object centre at (A) : 16.57400 1.520000 11.99650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0439450E-03 -6.4028716E-03 midg,1,midg; midg,igrid,midg -2.5780166E-03 -6.5898881E-03 1,midg,midg; igrid,midg,midg -1.3045917E-02 2.6783671E-02 gauss-seidel spectral radius is 0.9981756 estimated iterations to convergence 186 setup time was (sec) 0.5500000 now iterating at: 11:40:31 rms-change max change #iterations 3.284598 165.6985 at 10iterations 1.362818 62.78386 at 20iterations 0.5607168 25.02048 at 30iterations 0.2320255 8.321957 at 40iterations 9.6158952E-02 3.389534 at 50iterations 4.0065296E-02 1.345802 at 60iterations 1.6561223E-02 0.5902869 at 70iterations 6.8872985E-03 0.2402630 at 80iterations 2.8566795E-03 0.1114273 at 90iterations 1.1872899E-03 4.3889046E-02 at 100iterations 4.9350673E-04 1.9552231E-02 at 110iterations 2.0606919E-04 7.2784424E-03 at 120iterations finished qdiffx linear iterations at : 11:40:38 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.0606919E-04 7.2784424E-03 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 11:40:38 7.795u 0.200s 0:08.29 96.3% 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 Sun Oct 9 2011 at 11:40:39 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 = 3113 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: 2.403601 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): -16.75100 49.89900 ymin,ymax (A): -24.18900 27.22900 zmin,zma (A): -19.13400 43.12700 x,y,z range (A): 66.64999 51.41800 62.26100 scale (grids/A): 2.403601 object centre (A): 16.57400 1.520000 11.99650 number of atom coordinates read : 3113 total number of charged atoms : 3044 net assigned charge : -2.499987 assigned positive charge : 467.1192 centred at (gu) : 96.59228 92.70535 90.47942 assigned negative charge : -469.6212 centred at (gu) : 95.86874 93.03532 90.60146 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 156359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34716 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67208 mr = 102565 m= 19681 mr = 50082 m= 3344 mr = 14042 m= 197 mr = 2070 m= 5 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 77981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 24326 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) : 1.602401 object centre at (A) : 16.57400 1.520000 11.99650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2867155 -5.2229986E-02 midg,1,midg; midg,igrid,midg -7.7482082E-02 -8.9634389E-02 1,midg,midg; igrid,midg,midg -0.3688065 0.3428226 gauss-seidel spectral radius is 0.9991659 estimated iterations to convergence 273 setup time was (sec) 1.070000 now iterating at: 11:40:40 rms-change max change #iterations 8.929036 338.2567 at 10iterations 5.171139 133.4632 at 20iterations 2.979890 67.77650 at 30iterations 1.696515 44.94916 at 40iterations 0.9590365 23.64787 at 50iterations 0.5415542 11.75484 at 60iterations 0.3038190 7.050980 at 70iterations 0.1704593 3.505293 at 80iterations 9.5481463E-02 2.012976 at 90iterations 5.3288009E-02 1.114754 at 100iterations 2.9658252E-02 0.6105754 at 110iterations 1.6523808E-02 0.3253226 at 120iterations 9.1952700E-03 0.2030125 at 130iterations 5.1286276E-03 0.1075068 at 140iterations 2.8518313E-03 6.1203003E-02 at 150iterations 1.5850309E-03 3.1958580E-02 at 160iterations 8.8176562E-04 1.9466400E-02 at 170iterations 4.9020490E-04 1.1018753E-02 at 180iterations finished qdiffx linear iterations at : 11:40:51 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 4.9020490E-04 1.1018753E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 11:40:52 12.549u 0.201s 0:13.07 97.4% 0+0k 0+0io 0pf+0w