Mon Oct 10 19:37:34 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 19:37:34 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2873 !!! WARNING: GLM 105 has a net charge of -0.0940 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: 0.5726419 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): -16.97200 32.25900 ymin,ymax (A): 8.087999 57.74000 zmin,zma (A): 12.76400 74.93200 x,y,z range (A): 49.23100 49.65200 62.16800 scale (grids/A): 0.5726419 object centre (A): 7.643499 32.91400 43.84800 number of atom coordinates read : 2873 total number of charged atoms : 2728 net assigned charge : 1.906031 assigned positive charge : 428.2524 centred at (gu) : 90.27205 90.71619 90.10181 assigned negative charge : -426.3474 centred at (gu) : 90.30999 90.58337 90.22723 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6021 nv = 96 ne = 84 npr = 58319 no. pairs analyzed = 58319 no. exposed pairs = 3865 no. arc points = 27158 no. surface atoms = 1306 nbur = 1567 mkacc time = 0.1700000 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 = 1.512000 m= 302 mr = 2961 m= 4 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2704 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 7872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2927300E-09 -1.8346151E-09 midg,1,midg; midg,igrid,midg -1.6103757E-09 2.9316627E-09 1,midg,midg; igrid,midg,midg 8.7597196E-10 -3.4045669E-10 gauss-seidel spectral radius is 0.9842565 estimated iterations to convergence 65 setup time was (sec) 0.7300000 now iterating at: 19:37:35 rms-change max change #iterations 9.2444748E-02 16.74057 at 10iterations 6.9079483E-03 1.392853 at 20iterations 5.1853439E-04 8.3389282E-02 at 30iterations 4.0155679E-05 6.5155029E-03 at 40iterations 3.5302010E-06 5.8746338E-04 at 50iterations finished qdiffx linear iterations at : 19:37:38 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 3.5302010E-06 5.8746338E-04 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 19:37:39 4.317u 0.232s 0:05.14 88.3% 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 Mon Oct 10 2011 at 19:37:39 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2873 !!! WARNING: GLM 105 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.717926 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): -16.97200 32.25900 ymin,ymax (A): 8.087999 57.74000 zmin,zma (A): 12.76400 74.93200 x,y,z range (A): 49.23100 49.65200 62.16800 scale (grids/A): 1.717926 object centre (A): 7.643499 32.91400 43.84800 number of atom coordinates read : 2873 total number of charged atoms : 2728 net assigned charge : 1.906031 assigned positive charge : 428.2524 centred at (gu) : 90.81560 92.14818 90.30478 assigned negative charge : -426.3474 centred at (gu) : 90.92993 91.74982 90.68112 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 65115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27158 grid for indexing accessible points = 1.400000 m= 21137 mr = 42337 m= 2968 mr = 14470 m= 114 mr = 1638 m= 0 mr = 13 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 30876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21138 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) : 0.5726419 object centre at (A) : 7.643499 32.91400 43.84800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7638064E-03 -9.5524983E-03 midg,1,midg; midg,igrid,midg -1.5061334E-02 1.2952191E-02 1,midg,midg; igrid,midg,midg -4.3592160E-03 -2.5958140E-04 gauss-seidel spectral radius is 0.9983613 estimated iterations to convergence 196 setup time was (sec) 0.9700000 now iterating at: 19:37:40 rms-change max change #iterations 3.635029 184.3265 at 10iterations 1.572641 61.96632 at 20iterations 0.6856241 24.60759 at 30iterations 0.2989959 10.16138 at 40iterations 0.1293442 4.439844 at 50iterations 5.6603592E-02 1.947964 at 60iterations 2.4638286E-02 0.8647852 at 70iterations 1.0708737E-02 0.4267254 at 80iterations 4.6601002E-03 0.1529312 at 90iterations 2.0402609E-03 6.4880371E-02 at 100iterations 8.8782661E-04 2.9103279E-02 at 110iterations 3.8675594E-04 1.3978958E-02 at 120iterations finished qdiffx linear iterations at : 19:37:49 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 3.8675594E-04 1.3978958E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 19:37:49 9.458u 0.268s 0:10.11 96.0% 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 19:37:49 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2873 !!! WARNING: GLM 105 has a net charge of -0.0940 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: 2.576889 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): -16.97200 32.25900 ymin,ymax (A): 8.087999 57.74000 zmin,zma (A): 12.76400 74.93200 x,y,z range (A): 49.23100 49.65200 62.16800 scale (grids/A): 2.576889 object centre (A): 7.643499 32.91400 43.84800 number of atom coordinates read : 2873 total number of charged atoms : 2728 net assigned charge : 1.906031 assigned positive charge : 428.2524 centred at (gu) : 91.22327 93.22209 90.45697 assigned negative charge : -426.3474 centred at (gu) : 91.39470 92.62471 91.02167 start vw surface at 0.2200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 150638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27158 grid for indexing accessible points = 1.400000 m= 69932 mr = 103705 m= 23460 mr = 54489 m= 5055 mr = 17899 m= 437 mr = 3585 m= 3 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 69651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 21810 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) : 1.717926 object centre at (A) : 7.643499 32.91400 43.84800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9287049E-02 -4.6847604E-02 midg,1,midg; midg,igrid,midg -0.1974138 0.1613037 1,midg,midg; igrid,midg,midg -0.1121538 -4.6989888E-02 gauss-seidel spectral radius is 0.9991954 estimated iterations to convergence 278 setup time was (sec) 1.960000 now iterating at: 19:37:52 rms-change max change #iterations 9.115447 349.7653 at 10iterations 5.201899 133.0298 at 20iterations 2.968105 67.47430 at 30iterations 1.679208 38.46911 at 40iterations 0.9469900 21.70064 at 50iterations 0.5343105 10.56101 at 60iterations 0.2999980 6.190372 at 70iterations 0.1690675 3.404171 at 80iterations 9.4804220E-02 1.898197 at 90iterations 5.3305440E-02 1.121181 at 100iterations 2.9907279E-02 0.5995960 at 110iterations 1.6755626E-02 0.3295898 at 120iterations 9.4131669E-03 0.1898403 at 130iterations 5.2634068E-03 0.1039952 at 140iterations 2.9529447E-03 5.6592941E-02 at 150iterations 1.6550259E-03 3.5764694E-02 at 160iterations 9.2937727E-04 1.7658234E-02 at 170iterations 5.2038213E-04 1.0749817E-02 at 180iterations finished qdiffx linear iterations at : 19:38:05 total time elapsed so far: 14.89000 # loops : 180 mean,max change (kT/e) : 5.2038213E-04 1.0749817E-02 energy calculations done at 14.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.13000 DelPhi exited at 19:38:05 15.128u 0.247s 0:15.80 97.2% 0+0k 0+0io 0pf+0w