Sun Oct 9 20:00:25 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+sph.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 = amb.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 Sun Oct 9 2011 at 20:00:25 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5464 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5419559 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): 2.847000 68.31900 ymin,ymax (A): -8.841000 52.87800 zmin,zma (A): -2.314000 63.37400 x,y,z range (A): 65.47200 61.71900 65.68800 scale (grids/A): 0.5419559 object centre (A): 35.58300 22.01850 30.53000 number of atom coordinates read : 5464 total number of charged atoms : 5294 net assigned charge : 2.740054 assigned positive charge : 837.7369 centred at (gu) : 88.09590 89.20039 89.45842 assigned negative charge : -835.0031 centred at (gu) : 88.00550 89.19463 89.41732 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 10119 nv = 96 ne = 84 npr = 113639 no. pairs analyzed = 113639 no. exposed pairs = 6052 no. arc points = 41425 no. surface atoms = 2068 nbur = 3396 mkacc time = 0.2600000 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 = 1.596000 m= 365 mr = 5794 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4289 ## 535 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 13625 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1276556E-10 5.2828797E-10 midg,1,midg; midg,igrid,midg 1.3005266E-10 1.8932285E-10 1,midg,midg; igrid,midg,midg -1.3195279E-09 6.9824596E-10 gauss-seidel spectral radius is 0.9826195 estimated iterations to convergence 62 setup time was (sec) 0.7600000 now iterating at: 20:00:26 rms-change max change #iterations 0.1046374 17.83513 at 10iterations 1.2066158E-02 1.677261 at 20iterations 4.3333857E-03 0.6286049 at 30iterations 1.8875948E-03 0.2720642 at 40iterations 8.3023292E-04 0.1175995 at 50iterations finished qdiffx linear iterations at : 20:00:29 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 8.3023292E-04 0.1175995 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 20:00:29 3.580u 0.147s 0:04.03 92.3% 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 Sun Oct 9 2011 at 20:00:29 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5464 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.625868 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): 2.847000 68.31900 ymin,ymax (A): -8.841000 52.87800 zmin,zma (A): -2.314000 63.37400 x,y,z range (A): 65.47200 61.71900 65.68800 scale (grids/A): 1.625868 object centre (A): 35.58300 22.01850 30.53000 number of atom coordinates read : 5464 total number of charged atoms : 5294 net assigned charge : 2.740054 assigned positive charge : 837.7369 centred at (gu) : 84.28600 87.59977 88.37403 assigned negative charge : -835.0031 centred at (gu) : 84.01621 87.58379 88.25177 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 115080 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41425 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 36841 mr = 84067 m= 3906 mr = 26265 m= 130 mr = 1976 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.8100000 number of dielectric boundary points 43624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 495 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 40510 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) : 0.5419559 object centre at (A) : 35.58300 22.01850 30.53000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6802188E-02 1.7668311E-02 midg,1,midg; midg,igrid,midg 4.0026503E-03 8.1129204E-03 1,midg,midg; igrid,midg,midg -1.3310894E-02 1.0835570E-02 gauss-seidel spectral radius is 0.9983820 estimated iterations to convergence 197 setup time was (sec) 1.100000 now iterating at: 20:00:30 rms-change max change #iterations 4.756662 177.0798 at 10iterations 2.090383 63.07624 at 20iterations 0.9167051 26.18337 at 30iterations 0.4030564 13.94592 at 40iterations 0.1775971 4.845078 at 50iterations 7.9324260E-02 2.185959 at 60iterations 3.6336526E-02 1.019363 at 70iterations 1.7655682E-02 0.5393028 at 80iterations 9.6116001E-03 0.2894020 at 90iterations 5.9635933E-03 0.1821823 at 100iterations 4.0648743E-03 0.1174126 at 110iterations 2.9257282E-03 8.3351135E-02 at 120iterations finished qdiffx linear iterations at : 20:00:37 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.9257282E-03 8.3351135E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 20:00:37 7.842u 0.162s 0:08.34 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 Sun Oct 9 2011 at 20:00:37 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5464 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.438802 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): 2.847000 68.31900 ymin,ymax (A): -8.841000 52.87800 zmin,zma (A): -2.314000 63.37400 x,y,z range (A): 65.47200 61.71900 65.68800 scale (grids/A): 2.438802 object centre (A): 35.58300 22.01850 30.53000 number of atom coordinates read : 5464 total number of charged atoms : 5294 net assigned charge : 2.740054 assigned positive charge : 837.7369 centred at (gu) : 81.42876 86.39909 87.56055 assigned negative charge : -835.0031 centred at (gu) : 81.02448 86.37575 87.37748 start vw surface at 0.2300000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 268196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41425 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 128464 mr = 204864 m= 37105 mr = 104454 m= 6167 mr = 28328 m= 486 mr = 4057 m= 6 mr = 254 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 128 time to turn everything in is 2.000000 number of dielectric boundary points 98467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 42285 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) : 1.625868 object centre at (A) : 35.58300 22.01850 30.53000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3263331 0.3724129 midg,1,midg; midg,igrid,midg -1.1369189E-02 3.8507152E-02 1,midg,midg; igrid,midg,midg -0.3846296 0.1677838 gauss-seidel spectral radius is 0.9992386 estimated iterations to convergence 286 setup time was (sec) 2.320000 now iterating at: 20:00:40 rms-change max change #iterations 12.19574 380.7423 at 10iterations 7.138981 151.9286 at 20iterations 4.151940 79.85872 at 30iterations 2.403440 48.59052 at 40iterations 1.389143 24.38925 at 50iterations 0.8013551 13.56824 at 60iterations 0.4596425 7.562790 at 70iterations 0.2642972 4.382372 at 80iterations 0.1516073 2.289520 at 90iterations 8.7489560E-02 1.380417 at 100iterations 5.0532095E-02 0.8961239 at 110iterations 2.9534694E-02 0.5094700 at 120iterations 1.7628178E-02 0.3182068 at 130iterations 1.0932719E-02 0.2005005 at 140iterations 7.1477215E-03 0.1380424 at 150iterations 4.9910354E-03 9.9185944E-02 at 160iterations 3.7097486E-03 6.8367004E-02 at 170iterations 2.8928230E-03 5.2856445E-02 at 180iterations finished qdiffx linear iterations at : 20:00:51 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 2.8928230E-03 5.2856445E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 20:00:51 13.577u 0.168s 0:14.04 97.7% 0+0k 0+0io 0pf+0w