Tue Oct 11 06:49:47 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 Tue Oct 11 2011 at 06:49:47 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2946 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: HIR 259 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5721541 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): -16.88000 45.34100 ymin,ymax (A): 21.94000 79.21900 zmin,zma (A): -71.25900 -23.21900 x,y,z range (A): 62.22100 57.27900 48.04000 scale (grids/A): 0.5721541 object centre (A): 14.23050 50.57950 -47.23900 number of atom coordinates read : 2946 total number of charged atoms : 2802 net assigned charge : -2.579989 assigned positive charge : 429.7957 centred at (gu) : 88.57417 89.60976 89.51808 assigned negative charge : -432.3763 centred at (gu) : 88.52347 89.71224 89.51141 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6401 nv = 96 ne = 84 npr = 60730 no. pairs analyzed = 60730 no. exposed pairs = 3705 no. arc points = 25665 no. surface atoms = 1259 nbur = 1687 mkacc time = 0.1200000 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= 321 mr = 3482 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2554 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8117 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9102279E-10 -2.7777070E-10 midg,1,midg; midg,igrid,midg 1.3675645E-09 -1.9331832E-09 1,midg,midg; igrid,midg,midg -1.7676062E-09 2.8521147E-10 gauss-seidel spectral radius is 0.9842367 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 06:49:48 rms-change max change #iterations 9.2554532E-02 16.06010 at 10iterations 7.1567348E-03 1.234200 at 20iterations 6.7186926E-04 0.1176682 at 30iterations 1.2093534E-04 2.9174805E-02 at 40iterations 3.0813590E-05 7.7762604E-03 at 50iterations finished qdiffx linear iterations at : 06:49:52 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 3.0813590E-05 7.7762604E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 06:49:53 4.652u 0.246s 0:06.07 80.5% 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 Tue Oct 11 2011 at 06:49:54 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2946 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: HIR 259 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.716462 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): -16.88000 45.34100 ymin,ymax (A): 21.94000 79.21900 zmin,zma (A): -71.25900 -23.21900 x,y,z range (A): 62.22100 57.27900 48.04000 scale (grids/A): 1.716462 object centre (A): 14.23050 50.57950 -47.23900 number of atom coordinates read : 2946 total number of charged atoms : 2802 net assigned charge : -2.579989 assigned positive charge : 429.7957 centred at (gu) : 85.72199 88.82877 88.55361 assigned negative charge : -432.3763 centred at (gu) : 85.57037 89.13620 88.53408 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25665 grid for indexing accessible points = 1.400000 m= 23819 mr = 47745 m= 3095 mr = 17174 m= 123 mr = 1812 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21702 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) : 0.5721541 object centre at (A) : 14.23050 50.57950 -47.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1346917E-02 1.0146677E-02 midg,1,midg; midg,igrid,midg -5.3977692E-03 1.0873466E-02 1,midg,midg; igrid,midg,midg -3.2483671E-02 -2.8280163E-02 gauss-seidel spectral radius is 0.9983622 estimated iterations to convergence 196 setup time was (sec) 0.9100000 now iterating at: 06:49:55 rms-change max change #iterations 3.643763 151.8652 at 10iterations 1.587433 58.51611 at 20iterations 0.6890414 24.24316 at 30iterations 0.3014065 10.47534 at 40iterations 0.1307612 5.057049 at 50iterations 5.7436198E-02 1.973960 at 60iterations 2.4941258E-02 0.8735332 at 70iterations 1.0930268E-02 0.3738022 at 80iterations 4.8035351E-03 0.1840134 at 90iterations 2.1135465E-03 8.3120346E-02 at 100iterations 9.4085478E-04 3.4246445E-02 at 110iterations 4.2825550E-04 1.5155792E-02 at 120iterations finished qdiffx linear iterations at : 06:50:05 total time elapsed so far: 10.56000 # loops : 120 mean,max change (kT/e) : 4.2825550E-04 1.5155792E-02 energy calculations done at 10.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.74000 DelPhi exited at 06:50:06 10.740u 0.325s 0:11.87 93.1% 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 Tue Oct 11 2011 at 06:50:06 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2946 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: HIR 259 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.574693 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): -16.88000 45.34100 ymin,ymax (A): 21.94000 79.21900 zmin,zma (A): -71.25900 -23.21900 x,y,z range (A): 62.22100 57.27900 48.04000 scale (grids/A): 2.574693 object centre (A): 14.23050 50.57950 -47.23900 number of atom coordinates read : 2946 total number of charged atoms : 2802 net assigned charge : -2.579989 assigned positive charge : 429.7957 centred at (gu) : 83.58285 88.24310 87.83014 assigned negative charge : -432.3763 centred at (gu) : 83.35545 88.70438 87.80106 start vw surface at 0.1800000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 161211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25665 grid for indexing accessible points = 1.400000 m= 78590 mr = 116177 m= 26315 mr = 63687 m= 5265 mr = 20875 m= 526 mr = 3734 m= 11 mr = 315 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 67130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 22405 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) : 1.716462 object centre at (A) : 14.23050 50.57950 -47.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1988146 0.1531530 midg,1,midg; midg,igrid,midg -6.1060548E-02 0.1870087 1,midg,midg; igrid,midg,midg -0.4613462 -0.6095636 gauss-seidel spectral radius is 0.9991955 estimated iterations to convergence 278 setup time was (sec) 1.600000 now iterating at: 06:50:07 rms-change max change #iterations 9.135440 273.2409 at 10iterations 5.206327 126.4423 at 20iterations 2.954571 76.90110 at 30iterations 1.673323 36.61262 at 40iterations 0.9452326 19.70802 at 50iterations 0.5329253 10.09853 at 60iterations 0.3001838 5.975031 at 70iterations 0.1687765 3.205997 at 80iterations 9.4713382E-02 1.726428 at 90iterations 5.3150654E-02 1.109062 at 100iterations 2.9804403E-02 0.5432318 at 110iterations 1.6714798E-02 0.3171043 at 120iterations 9.3998676E-03 0.1797199 at 130iterations 5.2577788E-03 9.9760056E-02 at 140iterations 2.9524821E-03 5.7693481E-02 at 150iterations 1.6543976E-03 3.2548904E-02 at 160iterations 9.2890614E-04 1.8584251E-02 at 170iterations 5.2298384E-04 9.6759796E-03 at 180iterations finished qdiffx linear iterations at : 06:50:17 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 5.2298384E-04 9.6759796E-03 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 06:50:18 11.655u 0.211s 0:12.22 97.0% 0+0k 0+0io 0pf+0w