Sat Oct 8 12:13:58 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 8 2011 at 12:13:58 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2477 !!! WARNING: HIR 182 has a net charge of 0.5140 !!! WARNING: HIR 186 has a net charge of 0.5140 !!! WARNING: HIR 192 has a net charge of 0.5140 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: 0.6463795 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): -24.56400 30.51200 ymin,ymax (A): -5.296000 39.90100 zmin,zma (A): 8.447001 50.83800 x,y,z range (A): 55.07600 45.19700 42.39100 scale (grids/A): 0.6463795 object centre (A): 2.973999 17.30250 29.64250 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.957993 assigned positive charge : 382.1724 centred at (gu) : 89.95531 89.21549 91.00535 assigned negative charge : -384.1306 centred at (gu) : 90.06606 89.08788 91.01915 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6903 nv = 96 ne = 84 npr = 50729 no. pairs analyzed = 50729 no. exposed pairs = 2903 no. arc points = 21163 no. surface atoms = 975 nbur = 1502 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 3833 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.2800000 number of dielectric boundary points 3370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2031 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8227 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1093568E-09 -6.3173862E-09 midg,1,midg; midg,igrid,midg -2.4800396E-08 1.1807888E-08 1,midg,midg; igrid,midg,midg 1.1875550E-08 -1.8392807E-08 gauss-seidel spectral radius is 0.9875863 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 12:13:59 rms-change max change #iterations 0.1561928 24.10027 at 10iterations 1.5818242E-02 2.090592 at 20iterations 1.6035292E-03 0.2441940 at 30iterations 1.6078750E-04 2.2811737E-02 at 40iterations 1.6469085E-05 2.2239685E-03 at 50iterations finished qdiffx linear iterations at : 12:14:03 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.6469085E-05 2.2239685E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 12:14:03 4.209u 0.262s 0:04.77 93.5% 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 8 2011 at 12:14:03 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2477 !!! WARNING: HIR 182 has a net charge of 0.5140 !!! WARNING: HIR 186 has a net charge of 0.5140 !!! WARNING: HIR 192 has a net charge of 0.5140 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: 1.939139 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): -24.56400 30.51200 ymin,ymax (A): -5.296000 39.90100 zmin,zma (A): 8.447001 50.83800 x,y,z range (A): 55.07600 45.19700 42.39100 scale (grids/A): 1.939139 object centre (A): 2.973999 17.30250 29.64250 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.957993 assigned positive charge : 382.1724 centred at (gu) : 89.86574 87.64636 93.01597 assigned negative charge : -384.1306 centred at (gu) : 90.19806 87.26337 93.05711 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 74450 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21163 grid for indexing accessible points = 1.400000 m= 25946 mr = 51886 m= 4315 mr = 19173 m= 339 mr = 2828 m= 5 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1634 time to turn everything in is 0.5300000 number of dielectric boundary points 31017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18412 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) : 0.6463795 object centre at (A) : 2.973999 17.30250 29.64250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7841247E-03 -1.6712973E-02 midg,1,midg; midg,igrid,midg -1.9573113E-02 3.9856611E-03 1,midg,midg; igrid,midg,midg 2.4992710E-02 -4.9867671E-02 gauss-seidel spectral radius is 0.9986672 estimated iterations to convergence 217 setup time was (sec) 0.8500000 now iterating at: 12:14:04 rms-change max change #iterations 4.410218 175.8375 at 10iterations 2.079723 71.91928 at 20iterations 0.9838575 31.29289 at 30iterations 0.4646047 15.77866 at 40iterations 0.2192493 7.101026 at 50iterations 0.1034881 3.189341 at 60iterations 4.8855476E-02 1.741558 at 70iterations 2.3104694E-02 0.7133913 at 80iterations 1.0921648E-02 0.3804913 at 90iterations 5.1567648E-03 0.1514320 at 100iterations 2.4420870E-03 8.2197189E-02 at 110iterations 1.1536608E-03 3.4277916E-02 at 120iterations finished qdiffx linear iterations at : 12:14:13 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 1.1536608E-03 3.4277916E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 12:14:14 9.721u 0.289s 0:10.31 96.9% 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 8 2011 at 12:14:14 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2477 !!! WARNING: HIR 182 has a net charge of 0.5140 !!! WARNING: HIR 186 has a net charge of 0.5140 !!! WARNING: HIR 192 has a net charge of 0.5140 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: 2.908708 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): -24.56400 30.51200 ymin,ymax (A): -5.296000 39.90100 zmin,zma (A): 8.447001 50.83800 x,y,z range (A): 55.07600 45.19700 42.39100 scale (grids/A): 2.908708 object centre (A): 2.973999 17.30250 29.64250 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.957993 assigned positive charge : 382.1724 centred at (gu) : 89.79854 86.46941 94.52394 assigned negative charge : -384.1306 centred at (gu) : 90.29713 85.89505 94.58556 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 172606 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21163 grid for indexing accessible points = 1.400000 m= 84855 mr = 125925 m= 30248 mr = 69754 m= 7790 mr = 24339 m= 1394 mr = 5950 m= 106 mr = 1029 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 5270 time to turn everything in is 1.420000 number of dielectric boundary points 69952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 18694 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) : 1.939139 object centre at (A) : 2.973999 17.30250 29.64250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1354563E-02 -0.2848461 midg,1,midg; midg,igrid,midg -0.2105063 -1.5330283E-02 1,midg,midg; igrid,midg,midg 0.2696464 -0.7343321 gauss-seidel spectral radius is 0.9992621 estimated iterations to convergence 291 setup time was (sec) 1.770000 now iterating at: 12:14:16 rms-change max change #iterations 10.07391 396.5743 at 10iterations 5.830647 120.4704 at 20iterations 3.357528 71.68800 at 30iterations 1.930539 41.71954 at 40iterations 1.111934 19.51995 at 50iterations 0.6386631 11.33351 at 60iterations 0.3668219 6.383032 at 70iterations 0.2110482 4.087831 at 80iterations 0.1208405 2.111981 at 90iterations 6.9508485E-02 1.248831 at 100iterations 3.9878737E-02 0.7889862 at 110iterations 2.2897875E-02 0.4313765 at 120iterations 1.3133334E-02 0.2297287 at 130iterations 7.5322110E-03 0.1462698 at 140iterations 4.3290816E-03 7.3760986E-02 at 150iterations 2.4884825E-03 5.0879478E-02 at 160iterations 1.4282931E-03 2.5364876E-02 at 170iterations 8.1938319E-04 1.3956070E-02 at 180iterations finished qdiffx linear iterations at : 12:14:29 total time elapsed so far: 15.32000 # loops : 180 mean,max change (kT/e) : 8.1938319E-04 1.3956070E-02 energy calculations done at 15.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.51000 DelPhi exited at 12:14:30 15.507u 0.279s 0:16.11 97.8% 0+0k 0+0io 0pf+0w