Tue Nov 22 14:22:05 PST 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 Nov 22 2011 at 14:22:10 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5958059 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): -24.91000 34.84100 ymin,ymax (A): -18.50200 20.24600 zmin,zma (A): -4.089000 38.84700 x,y,z range (A): 59.75100 38.74800 42.93600 scale (grids/A): 0.5958059 object centre (A): 4.965502 0.8720007 17.37900 number of atom coordinates read : 1969 total number of charged atoms : 1837 net assigned charge : 3.000005 assigned positive charge : 292.9940 centred at (gu) : 90.03178 90.11807 90.40189 assigned negative charge : -289.9943 centred at (gu) : 90.04794 90.21017 90.53255 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4660 nv = 96 ne = 84 npr = 40298 no. pairs analyzed = 40298 no. exposed pairs = 2572 no. arc points = 17511 no. surface atoms = 881 nbur = 1088 mkacc time = 8.9999996E-02 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 = 1.456000 m= 220 mr = 2479 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1772 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5743 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8499928E-09 -2.2401558E-09 midg,1,midg; midg,igrid,midg 3.2333145E-09 -1.1187257E-09 1,midg,midg; igrid,midg,midg 1.5162543E-09 7.5883116E-10 gauss-seidel spectral radius is 0.9853691 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 14:22:13 rms-change max change #iterations 9.2271835E-02 16.60620 at 10iterations 7.6448694E-03 1.219917 at 20iterations 6.4080220E-04 0.1001396 at 30iterations 5.2039220E-05 7.9727173E-03 at 40iterations 4.3857890E-06 7.4958801E-04 at 50iterations finished qdiffx linear iterations at : 14:22:20 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 4.3857890E-06 7.4958801E-04 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 14:22:21 3.053u 0.118s 0:11.10 28.4% 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 Tue Nov 22 2011 at 14:22:22 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.787418 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): -24.91000 34.84100 ymin,ymax (A): -18.50200 20.24600 zmin,zma (A): -4.089000 38.84700 x,y,z range (A): 59.75100 38.74800 42.93600 scale (grids/A): 1.787418 object centre (A): 4.965502 0.8720007 17.37900 number of atom coordinates read : 1969 total number of charged atoms : 1837 net assigned charge : 3.000005 assigned positive charge : 292.9940 centred at (gu) : 90.09514 90.35429 91.20564 assigned negative charge : -289.9943 centred at (gu) : 90.14397 90.63077 91.59796 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 50281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17511 grid for indexing accessible points = 1.400000 m= 17268 mr = 33841 m= 2250 mr = 12557 m= 93 mr = 1266 m= 0 mr = 26 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 22202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 14359 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) : 0.5958059 object centre at (A) : 4.965502 0.8720007 17.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5198666E-03 -5.0241812E-03 midg,1,midg; midg,igrid,midg 7.1715559E-03 -2.9302228E-03 1,midg,midg; igrid,midg,midg 3.4639023E-02 2.8243957E-02 gauss-seidel spectral radius is 0.9983760 estimated iterations to convergence 197 setup time was (sec) 0.6000000 now iterating at: 14:22:27 rms-change max change #iterations 3.206073 153.1212 at 10iterations 1.395508 52.57956 at 20iterations 0.6101976 26.35991 at 30iterations 0.2654176 11.00450 at 40iterations 0.1156768 4.345103 at 50iterations 5.0628781E-02 1.902527 at 60iterations 2.2136468E-02 0.9220648 at 70iterations 9.6785342E-03 0.3950768 at 80iterations 4.2384961E-03 0.1730804 at 90iterations 1.8452100E-03 6.3636780E-02 at 100iterations 8.0882449E-04 2.7642250E-02 at 110iterations 3.5350575E-04 1.3565063E-02 at 120iterations finished qdiffx linear iterations at : 14:22:44 total time elapsed so far: 6.420000 # loops : 120 mean,max change (kT/e) : 3.5350575E-04 1.3565063E-02 energy calculations done at 6.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.590000 DelPhi exited at 14:22:46 6.596u 0.151s 0:23.70 28.4% 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 Tue Nov 22 2011 at 14:22:47 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.681127 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): -24.91000 34.84100 ymin,ymax (A): -18.50200 20.24600 zmin,zma (A): -4.089000 38.84700 x,y,z range (A): 59.75100 38.74800 42.93600 scale (grids/A): 2.681127 object centre (A): 4.965502 0.8720007 17.37900 number of atom coordinates read : 1969 total number of charged atoms : 1837 net assigned charge : 3.000005 assigned positive charge : 292.9940 centred at (gu) : 90.14267 90.53143 91.80843 assigned negative charge : -289.9943 centred at (gu) : 90.21593 90.94619 92.39704 start vw surface at 0.1200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 116085 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17511 grid for indexing accessible points = 1.400000 m= 57014 mr = 82200 m= 19320 mr = 46088 m= 3809 mr = 15374 m= 349 mr = 2682 m= 22 mr = 173 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 50068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 14693 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) : 1.787418 object centre at (A) : 4.965502 0.8720007 17.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6221761E-02 -3.7399516E-02 midg,1,midg; midg,igrid,midg 6.3705921E-02 -3.0665068E-02 1,midg,midg; igrid,midg,midg 0.4172074 0.4301743 gauss-seidel spectral radius is 0.9991677 estimated iterations to convergence 274 setup time was (sec) 1.150000 now iterating at: 14:22:54 rms-change max change #iterations 7.838207 278.1199 at 10iterations 4.468281 122.7691 at 20iterations 2.522508 84.42195 at 30iterations 1.413890 40.21613 at 40iterations 0.7901596 21.16469 at 50iterations 0.4422541 11.75703 at 60iterations 0.2466247 5.715546 at 70iterations 0.1377237 3.233907 at 80iterations 7.6544814E-02 1.756331 at 90iterations 4.2707291E-02 0.9603844 at 100iterations 2.3733372E-02 0.5645638 at 110iterations 1.3174086E-02 0.3084259 at 120iterations 7.3320521E-03 0.1600962 at 130iterations 4.0675602E-03 9.0525150E-02 at 140iterations 2.2628636E-03 5.2148461E-02 at 150iterations 1.2560738E-03 2.9756546E-02 at 160iterations 6.9703959E-04 1.4903069E-02 at 170iterations 3.8667279E-04 8.2473755E-03 at 180iterations finished qdiffx linear iterations at : 14:23:24 total time elapsed so far: 11.40000 # loops : 180 mean,max change (kT/e) : 3.8667279E-04 8.2473755E-03 energy calculations done at 11.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 14:23:26 11.580u 0.142s 0:38.90 30.1% 0+0k 0+0io 0pf+0w