Sat Oct 15 15:18:40 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+sph2.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 = amb2.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 Sat Oct 15 2011 at 15:18:40 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 !!! WARNING: HIR 75 has a net charge of 0.5140 !!! WARNING: SEP 237 has a net charge of -0.4750 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: 0.6548090 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): -4.398000 45.23300 ymin,ymax (A): -7.889000 42.71500 zmin,zma (A): -71.55800 -17.19100 x,y,z range (A): 49.63100 50.60400 54.36700 scale (grids/A): 0.6548090 object centre (A): 20.41750 17.41300 -44.37450 number of atom coordinates read : 2917 total number of charged atoms : 2768 net assigned charge : 5.539024 assigned positive charge : 445.8076 centred at (gu) : 89.00179 89.04710 87.75016 assigned negative charge : -440.2691 centred at (gu) : 89.14673 89.21926 87.81003 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7879 nv = 96 ne = 84 npr = 59528 no. pairs analyzed = 59528 no. exposed pairs = 4059 no. arc points = 27697 no. surface atoms = 1353 nbur = 1564 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 3750 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3900000 number of dielectric boundary points 4594 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2637 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9696 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6639598E-08 -1.2844202E-10 midg,1,midg; midg,igrid,midg 5.4054265E-08 -1.8644638E-08 1,midg,midg; igrid,midg,midg 4.8221608E-08 -1.4023046E-08 gauss-seidel spectral radius is 0.9879429 estimated iterations to convergence 74 setup time was (sec) 0.6700000 now iterating at: 15:18:41 rms-change max change #iterations 0.1705280 21.76251 at 10iterations 1.7799648E-02 2.382252 at 20iterations 2.0377303E-03 0.3356133 at 30iterations 3.3125989E-04 5.6175232E-02 at 40iterations 9.9247824E-05 1.4583588E-02 at 50iterations finished qdiffx linear iterations at : 15:18:44 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 9.9247824E-05 1.4583588E-02 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 15:18:45 4.252u 0.275s 0:05.01 90.2% 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 Sat Oct 15 2011 at 15:18:45 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 !!! WARNING: HIR 75 has a net charge of 0.5140 !!! WARNING: SEP 237 has a net charge of -0.4750 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: 1.964427 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): -4.398000 45.23300 ymin,ymax (A): -7.889000 42.71500 zmin,zma (A): -71.55800 -17.19100 x,y,z range (A): 49.63100 50.60400 54.36700 scale (grids/A): 1.964427 object centre (A): 20.41750 17.41300 -44.37450 number of atom coordinates read : 2917 total number of charged atoms : 2768 net assigned charge : 5.539024 assigned positive charge : 445.8076 centred at (gu) : 87.00489 87.14109 83.25005 assigned negative charge : -440.2691 centred at (gu) : 87.43983 87.65739 83.42962 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 82568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27697 grid for indexing accessible points = 1.400000 m= 30751 mr = 52979 m= 6521 mr = 20943 m= 478 mr = 3953 m= 6 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 42293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 21848 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) : 0.6548090 object centre at (A) : 20.41750 17.41300 -44.37450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1347003 3.5431776E-02 midg,1,midg; midg,igrid,midg -1.0583685E-03 -1.6703177E-02 1,midg,midg; igrid,midg,midg 3.1597916E-02 -2.1667592E-02 gauss-seidel spectral radius is 0.9987522 estimated iterations to convergence 224 setup time was (sec) 1.110000 now iterating at: 15:18:47 rms-change max change #iterations 4.875916 203.9004 at 10iterations 2.355702 72.00830 at 20iterations 1.134335 38.54268 at 30iterations 0.5491468 16.82667 at 40iterations 0.2654567 8.260267 at 50iterations 0.1282314 4.067303 at 60iterations 6.2065326E-02 1.880447 at 70iterations 3.0113844E-02 0.9204597 at 80iterations 1.4605653E-02 0.4241180 at 90iterations 7.1057710E-03 0.2046185 at 100iterations 3.4593258E-03 0.1097608 at 110iterations 1.6986817E-03 4.6913147E-02 at 120iterations finished qdiffx linear iterations at : 15:18:55 total time elapsed so far: 9.910000 # loops : 120 mean,max change (kT/e) : 1.6986817E-03 4.6913147E-02 energy calculations done at 9.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.10000 DelPhi exited at 15:18:56 10.103u 0.344s 0:10.91 95.6% 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 Sat Oct 15 2011 at 15:18:56 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 !!! WARNING: HIR 75 has a net charge of 0.5140 !!! WARNING: SEP 237 has a net charge of -0.4750 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: 2.946640 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): -4.398000 45.23300 ymin,ymax (A): -7.889000 42.71500 zmin,zma (A): -71.55800 -17.19100 x,y,z range (A): 49.63100 50.60400 54.36700 scale (grids/A): 2.946640 object centre (A): 20.41750 17.41300 -44.37450 number of atom coordinates read : 2917 total number of charged atoms : 2768 net assigned charge : 5.539024 assigned positive charge : 445.8076 centred at (gu) : 85.50703 85.71136 79.87485 assigned negative charge : -440.2691 centred at (gu) : 86.15961 86.48593 80.14429 start vw surface at 0.1700000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 190058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27697 grid for indexing accessible points = 1.400000 m= 94327 mr = 129557 m= 39301 mr = 72641 m= 12109 mr = 30197 m= 2144 mr = 8819 m= 150 mr = 1375 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 95439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 22142 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) : 1.964427 object centre at (A) : 20.41750 17.41300 -44.37450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.478847 0.3444785 midg,1,midg; midg,igrid,midg -0.2109017 -8.5450731E-02 1,midg,midg; igrid,midg,midg 0.1925971 -0.1942318 gauss-seidel spectral radius is 0.9993062 estimated iterations to convergence 300 setup time was (sec) 2.460000 now iterating at: 15:18:59 rms-change max change #iterations 11.62725 357.9661 at 10iterations 7.065966 149.8937 at 20iterations 4.252983 94.38771 at 30iterations 2.554910 51.29705 at 40iterations 1.520911 31.51712 at 50iterations 0.9066802 18.03910 at 60iterations 0.5359319 9.658553 at 70iterations 0.3179440 5.799263 at 80iterations 0.1874246 3.394962 at 90iterations 0.1106072 1.863899 at 100iterations 6.5140672E-02 1.423906 at 110iterations 3.8327001E-02 0.6877403 at 120iterations 2.2560930E-02 0.4109688 at 130iterations 1.3277965E-02 0.2421703 at 140iterations 7.8110658E-03 0.1322861 at 150iterations 4.6150661E-03 7.9122543E-02 at 160iterations 2.7353789E-03 4.3830872E-02 at 170iterations 1.6390438E-03 2.9647350E-02 at 180iterations finished qdiffx linear iterations at : 15:19:14 total time elapsed so far: 17.54000 # loops : 180 mean,max change (kT/e) : 1.6390438E-03 2.9647350E-02 energy calculations done at 17.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.72000 DelPhi exited at 15:19:15 17.718u 0.350s 0:18.47 97.7% 0+0k 0+0io 0pf+0w