Mon Oct 10 14:15:09 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 Mon Oct 10 2011 at 14:15:09 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3189 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5761077 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): -9.073000 43.20600 ymin,ymax (A): -28.77300 25.55500 zmin,zma (A): 14.08200 75.87600 x,y,z range (A): 52.27900 54.32800 61.79400 scale (grids/A): 0.5761077 object centre (A): 17.06650 -1.608999 44.97900 number of atom coordinates read : 3189 total number of charged atoms : 3040 net assigned charge : -5.773973 assigned positive charge : 479.0654 centred at (gu) : 89.80713 91.98306 91.30556 assigned negative charge : -484.8406 centred at (gu) : 89.61788 91.87570 91.26234 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6805 nv = 96 ne = 84 npr = 65779 no. pairs analyzed = 65779 no. exposed pairs = 3868 no. arc points = 27133 no. surface atoms = 1295 nbur = 1894 mkacc time = 0.1900000 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 = 1.484000 m= 307 mr = 3695 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3900000 number of dielectric boundary points 3395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2763 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8870 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5173812E-09 -3.0850245E-10 midg,1,midg; midg,igrid,midg -2.1543021E-09 1.7861536E-09 1,midg,midg; igrid,midg,midg -5.4451172E-09 2.6091409E-09 gauss-seidel spectral radius is 0.9844621 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 14:15:10 rms-change max change #iterations 0.1011032 14.14256 at 10iterations 8.0852453E-03 1.200117 at 20iterations 1.1242486E-03 0.2201538 at 30iterations 4.3625897E-04 9.4871521E-02 at 40iterations 1.9250539E-04 4.2320251E-02 at 50iterations finished qdiffx linear iterations at : 14:15:13 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.9250539E-04 4.2320251E-02 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 14:15:14 4.142u 0.271s 0:04.82 91.4% 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 Mon Oct 10 2011 at 14:15:14 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3189 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.728323 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): -9.073000 43.20600 ymin,ymax (A): -28.77300 25.55500 zmin,zma (A): 14.08200 75.87600 x,y,z range (A): 52.27900 54.32800 61.79400 scale (grids/A): 1.728323 object centre (A): 17.06650 -1.608999 44.97900 number of atom coordinates read : 3189 total number of charged atoms : 3040 net assigned charge : -5.773973 assigned positive charge : 479.0654 centred at (gu) : 89.42023 95.94801 93.91556 assigned negative charge : -484.8406 centred at (gu) : 88.85311 95.62649 93.78659 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 75147 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27133 grid for indexing accessible points = 1.400000 m= 24068 mr = 52014 m= 2929 mr = 17225 m= 122 mr = 1684 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1200 time to turn everything in is 0.6700000 number of dielectric boundary points 31320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 299 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 23563 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) : 0.5761077 object centre at (A) : 17.06650 -1.608999 44.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9401768E-02 8.6215613E-03 midg,1,midg; midg,igrid,midg -1.9976772E-02 -4.1219275E-03 1,midg,midg; igrid,midg,midg -2.6068000E-02 -2.6375879E-04 gauss-seidel spectral radius is 0.9984019 estimated iterations to convergence 198 setup time was (sec) 0.9700000 now iterating at: 14:15:15 rms-change max change #iterations 3.955732 149.4327 at 10iterations 1.736396 59.73515 at 20iterations 0.7634392 27.14890 at 30iterations 0.3368390 11.00374 at 40iterations 0.1485936 5.792498 at 50iterations 6.5381981E-02 2.497803 at 60iterations 2.8993294E-02 0.9243598 at 70iterations 1.2936754E-02 0.4304352 at 80iterations 5.9778071E-03 0.2322903 at 90iterations 2.9624428E-03 0.1139832 at 100iterations 1.6508237E-03 6.9149017E-02 at 110iterations 1.0621671E-03 4.6867371E-02 at 120iterations finished qdiffx linear iterations at : 14:15:23 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 1.0621671E-03 4.6867371E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 14:15:24 9.521u 0.287s 0:10.21 95.9% 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 Mon Oct 10 2011 at 14:15:24 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3189 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.592485 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): -9.073000 43.20600 ymin,ymax (A): -28.77300 25.55500 zmin,zma (A): 14.08200 75.87600 x,y,z range (A): 52.27900 54.32800 61.79400 scale (grids/A): 2.592485 object centre (A): 17.06650 -1.608999 44.97900 number of atom coordinates read : 3189 total number of charged atoms : 3040 net assigned charge : -5.773973 assigned positive charge : 479.0654 centred at (gu) : 89.12997 98.92184 95.87302 assigned negative charge : -484.8406 centred at (gu) : 88.27965 98.43965 95.67979 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 174206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27133 grid for indexing accessible points = 1.400000 m= 81798 mr = 126744 m= 25421 mr = 65978 m= 4911 mr = 19840 m= 439 mr = 3471 m= 16 mr = 245 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 3936 time to turn everything in is 1.650000 number of dielectric boundary points 70513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 24297 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) : 1.728323 object centre at (A) : 17.06650 -1.608999 44.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2339027 4.4286299E-02 midg,1,midg; midg,igrid,midg -0.2985077 -3.4667965E-02 1,midg,midg; igrid,midg,midg -0.2047163 -6.4521417E-02 gauss-seidel spectral radius is 0.9992048 estimated iterations to convergence 280 setup time was (sec) 1.980000 now iterating at: 14:15:26 rms-change max change #iterations 9.821321 332.4281 at 10iterations 5.656528 152.9143 at 20iterations 3.242678 77.31995 at 30iterations 1.849836 40.37710 at 40iterations 1.049972 22.06007 at 50iterations 0.5964372 13.13087 at 60iterations 0.3383793 6.872093 at 70iterations 0.1915673 4.541290 at 80iterations 0.1083752 2.145687 at 90iterations 6.1298184E-02 1.163857 at 100iterations 3.4611829E-02 0.6695337 at 110iterations 1.9568473E-02 0.3961368 at 120iterations 1.1084614E-02 0.2110481 at 130iterations 6.3175363E-03 0.1431980 at 140iterations 3.6611315E-03 7.5107574E-02 at 150iterations 2.1720577E-03 4.5645714E-02 at 160iterations 1.3557666E-03 3.4187317E-02 at 170iterations 9.1005466E-04 2.1903992E-02 at 180iterations finished qdiffx linear iterations at : 14:15:40 total time elapsed so far: 15.76000 # loops : 180 mean,max change (kT/e) : 9.1005466E-04 2.1903992E-02 energy calculations done at 15.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 14:15:41 15.943u 0.313s 0:16.59 97.9% 0+0k 0+0io 0pf+0w