Sat Oct 8 11:33:22 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 11:33:22 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3467 !!! WARNING: GLM 520 has a net charge of -0.0940 !!! WARNING: HIT 906 has a net charge of 0.5140 !!! WARNING: ALA 1069 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5302985 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): -16.18600 39.01400 ymin,ymax (A): -19.74200 34.91400 zmin,zma (A): -47.08000 20.05200 x,y,z range (A): 55.20000 54.65600 67.13200 scale (grids/A): 0.5302985 object centre (A): 11.41400 7.586000 -13.51400 number of atom coordinates read : 3467 total number of charged atoms : 3351 net assigned charge : 0.1480188 assigned positive charge : 524.0522 centred at (gu) : 91.24089 89.30280 89.08290 assigned negative charge : -523.9058 centred at (gu) : 91.22470 89.23858 88.97256 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6523 nv = 96 ne = 84 npr = 66666 no. pairs analyzed = 66666 no. exposed pairs = 4795 no. arc points = 33779 no. surface atoms = 1613 nbur = 1854 mkacc time = 0.1500000 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 = 1.624000 m= 266 mr = 3141 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3402 ## 440 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9209848E-10 3.7564285E-10 midg,1,midg; midg,igrid,midg -3.1772099E-10 2.3656058E-10 1,midg,midg; igrid,midg,midg -4.2104827E-11 1.1071807E-10 gauss-seidel spectral radius is 0.9817284 estimated iterations to convergence 61 setup time was (sec) 0.6300000 now iterating at: 11:33:22 rms-change max change #iterations 6.5646008E-02 11.82934 at 10iterations 4.0519321E-03 0.6733322 at 20iterations 2.4927515E-04 4.4523239E-02 at 30iterations 1.6059372E-05 2.7623177E-03 at 40iterations 1.1564313E-06 1.5640259E-04 at 50iterations finished qdiffx linear iterations at : 11:33:25 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.1564313E-06 1.5640259E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 11:33:26 3.493u 0.154s 0:03.96 91.9% 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 11:33:26 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3467 !!! WARNING: GLM 520 has a net charge of -0.0940 !!! WARNING: HIT 906 has a net charge of 0.5140 !!! WARNING: ALA 1069 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.590896 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): -16.18600 39.01400 ymin,ymax (A): -19.74200 34.91400 zmin,zma (A): -47.08000 20.05200 x,y,z range (A): 55.20000 54.65600 67.13200 scale (grids/A): 1.590896 object centre (A): 11.41400 7.586000 -13.51400 number of atom coordinates read : 3467 total number of charged atoms : 3351 net assigned charge : 0.1480188 assigned positive charge : 524.0522 centred at (gu) : 93.72156 87.90773 87.24729 assigned negative charge : -523.9058 centred at (gu) : 93.67375 87.71545 86.91730 start vw surface at 0.2200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 72343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21776 mr = 47318 m= 2418 mr = 14223 m= 47 mr = 1175 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 33863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 366 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 25543 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) : 0.5302985 object centre at (A) : 11.41400 7.586000 -13.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0793929E-02 -5.7810294E-03 midg,1,midg; midg,igrid,midg -1.9224697E-03 2.8362351E-03 1,midg,midg; igrid,midg,midg 2.5409602E-03 3.2388461E-03 gauss-seidel spectral radius is 0.9981418 estimated iterations to convergence 184 setup time was (sec) 0.9000000 now iterating at: 11:33:27 rms-change max change #iterations 3.453602 160.3761 at 10iterations 1.422994 52.21943 at 20iterations 0.5879823 22.01379 at 30iterations 0.2423203 9.191610 at 40iterations 0.1003303 3.778301 at 50iterations 4.1206531E-02 1.528278 at 60iterations 1.7092139E-02 0.6082039 at 70iterations 7.0410040E-03 0.2398405 at 80iterations 2.9146101E-03 0.1068230 at 90iterations 1.2006517E-03 4.4371605E-02 at 100iterations 4.9654744E-04 1.6098022E-02 at 110iterations 2.0533722E-04 7.9498291E-03 at 120iterations finished qdiffx linear iterations at : 11:33:33 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 2.0533722E-04 7.9498291E-03 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 11:33:34 7.648u 0.164s 0:08.16 95.5% 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 11:33:34 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3467 !!! WARNING: GLM 520 has a net charge of -0.0940 !!! WARNING: HIT 906 has a net charge of 0.5140 !!! WARNING: ALA 1069 has a net charge of -0.2720 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: 2.386343 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): -16.18600 39.01400 ymin,ymax (A): -19.74200 34.91400 zmin,zma (A): -47.08000 20.05200 x,y,z range (A): 55.20000 54.65600 67.13200 scale (grids/A): 2.386343 object centre (A): 11.41400 7.586000 -13.51400 number of atom coordinates read : 3467 total number of charged atoms : 3351 net assigned charge : 0.1480188 assigned positive charge : 524.0522 centred at (gu) : 95.58240 86.86133 85.87083 assigned negative charge : -523.9058 centred at (gu) : 95.51039 86.57300 85.37591 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 167878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 75156 mr = 116266 m= 21290 mr = 57644 m= 3811 mr = 15441 m= 239 mr = 2506 m= 4 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.7900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 76430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 26766 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) : 1.590896 object centre at (A) : 11.41400 7.586000 -13.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5132389 -0.1030538 midg,1,midg; midg,igrid,midg -7.7254241E-03 2.0357048E-02 1,midg,midg; igrid,midg,midg 5.7894327E-02 5.1365633E-02 gauss-seidel spectral radius is 0.9991437 estimated iterations to convergence 270 setup time was (sec) 1.640000 now iterating at: 11:33:36 rms-change max change #iterations 9.263497 270.1066 at 10iterations 5.325732 151.4440 at 20iterations 3.022456 79.17094 at 30iterations 1.699995 48.94477 at 40iterations 0.9481874 21.65363 at 50iterations 0.5292278 12.66815 at 60iterations 0.2948077 7.013535 at 70iterations 0.1633211 3.842570 at 80iterations 9.0294585E-02 2.352164 at 90iterations 4.9909811E-02 1.195838 at 100iterations 2.7568499E-02 0.5925980 at 110iterations 1.5216194E-02 0.2929358 at 120iterations 8.3670495E-03 0.1671615 at 130iterations 4.6147713E-03 9.1535568E-02 at 140iterations 2.5413139E-03 4.7584534E-02 at 150iterations 1.3969257E-03 2.8164148E-02 at 160iterations 7.7069347E-04 1.5426636E-02 at 170iterations 4.2440958E-04 9.7579956E-03 at 180iterations finished qdiffx linear iterations at : 11:33:46 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 4.2440958E-04 9.7579956E-03 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 11:33:47 12.143u 0.182s 0:12.69 97.0% 0+0k 0+0io 0pf+0w