Mon Oct 10 14:03:56 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 14:03:57 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 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: 0.4949601 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): -12.22200 37.12000 ymin,ymax (A): -38.88100 25.01800 zmin,zma (A): -14.58000 57.34500 x,y,z range (A): 49.34200 63.89899 71.92500 scale (grids/A): 0.4949601 object centre (A): 12.44900 -6.931499 21.38250 number of atom coordinates read : 3109 total number of charged atoms : 2953 net assigned charge : 0.5000085 assigned positive charge : 464.8236 centred at (gu) : 89.95491 91.79799 88.83528 assigned negative charge : -464.3247 centred at (gu) : 89.97654 91.82142 88.80782 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 4958 nv = 96 ne = 84 npr = 59923 no. pairs analyzed = 59923 no. exposed pairs = 4286 no. arc points = 31235 no. surface atoms = 1452 nbur = 1657 mkacc time = 0.2100000 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 = 1.708000 m= 139 mr = 2218 m= 0 mr = 6 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 2873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3052 ## 543 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 6644 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6384438E-11 1.9770288E-11 midg,1,midg; midg,igrid,midg 1.4612046E-11 -2.5928960E-11 1,midg,midg; igrid,midg,midg 2.2542378E-11 -1.3941875E-11 gauss-seidel spectral radius is 0.9790313 estimated iterations to convergence 57 setup time was (sec) 0.8000000 now iterating at: 14:03:58 rms-change max change #iterations 4.4991914E-02 9.017159 at 10iterations 2.2399216E-03 0.4754696 at 20iterations 1.1976376E-04 2.1006405E-02 at 30iterations 8.2985271E-06 1.6098022E-03 at 40iterations 9.9606029E-07 2.1839142E-04 at 50iterations finished qdiffx linear iterations at : 14:04:02 total time elapsed so far: 4.700000 # loops : 50 mean,max change (kT/e) : 9.9606029E-07 2.1839142E-04 energy calculations done at 4.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.910000 DelPhi exited at 14:04:02 4.915u 0.418s 0:05.73 92.8% 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 14:04:02 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 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: 1.484880 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): -12.22200 37.12000 ymin,ymax (A): -38.88100 25.01800 zmin,zma (A): -14.58000 57.34500 x,y,z range (A): 49.34200 63.89899 71.92500 scale (grids/A): 1.484880 object centre (A): 12.44900 -6.931499 21.38250 number of atom coordinates read : 3109 total number of charged atoms : 2953 net assigned charge : 0.5000085 assigned positive charge : 464.8236 centred at (gu) : 89.86398 95.39300 86.50501 assigned negative charge : -464.3247 centred at (gu) : 89.92910 95.46387 86.42284 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 55162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31235 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 13268 mr = 34182 m= 845 mr = 7948 m= 8 mr = 280 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 26873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 461 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21877 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) : 0.4949601 object centre at (A) : 12.44900 -6.931499 21.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6869717E-03 7.7060220E-04 midg,1,midg; midg,igrid,midg 2.7572692E-03 1.2020828E-02 1,midg,midg; igrid,midg,midg -7.0783397E-04 -1.0639509E-03 gauss-seidel spectral radius is 0.9978175 estimated iterations to convergence 170 setup time was (sec) 0.9300000 now iterating at: 14:04:04 rms-change max change #iterations 2.714458 134.2535 at 10iterations 1.036165 50.33201 at 20iterations 0.3936355 18.60127 at 30iterations 0.1516455 6.354874 at 40iterations 5.7891481E-02 2.459199 at 50iterations 2.1983199E-02 0.8401518 at 60iterations 8.4159747E-03 0.3512859 at 70iterations 3.2199444E-03 0.1378496 at 80iterations 1.2358212E-03 5.6227565E-02 at 90iterations 4.7312735E-04 2.0007491E-02 at 100iterations 1.8067847E-04 7.3480606E-03 at 110iterations 6.9564361E-05 2.9582977E-03 at 120iterations finished qdiffx linear iterations at : 14:04:13 total time elapsed so far: 10.07000 # loops : 120 mean,max change (kT/e) : 6.9564361E-05 2.9582977E-03 energy calculations done at 10.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 14:04:13 10.285u 0.443s 0:11.10 96.5% 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 Mon Oct 10 2011 at 14:04:14 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 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: 2.227320 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): -12.22200 37.12000 ymin,ymax (A): -38.88100 25.01800 zmin,zma (A): -14.58000 57.34500 x,y,z range (A): 49.34200 63.89899 71.92500 scale (grids/A): 2.227320 object centre (A): 12.44900 -6.931499 21.38250 number of atom coordinates read : 3109 total number of charged atoms : 2953 net assigned charge : 0.5000085 assigned positive charge : 464.8236 centred at (gu) : 89.79567 98.08935 84.75719 assigned negative charge : -464.3247 centred at (gu) : 89.89357 98.19544 84.63420 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 129021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31235 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 49447 mr = 85387 m= 10148 mr = 36292 m= 1029 mr = 6719 m= 33 mr = 527 m= 0 mr = 5 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 60748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 23527 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) : 1.484880 object centre at (A) : 12.44900 -6.931499 21.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2286262 3.7570111E-02 midg,1,midg; midg,igrid,midg 3.4717530E-02 0.3544570 1,midg,midg; igrid,midg,midg -6.2010167E-03 -3.1261865E-02 gauss-seidel spectral radius is 0.9990260 estimated iterations to convergence 253 setup time was (sec) 1.710000 now iterating at: 14:04:16 rms-change max change #iterations 7.561044 234.3417 at 10iterations 4.104931 118.0023 at 20iterations 2.224911 60.28872 at 30iterations 1.190766 31.08572 at 40iterations 0.6364967 16.50869 at 50iterations 0.3385227 8.919990 at 60iterations 0.1799159 4.046251 at 70iterations 9.5713004E-02 2.426994 at 80iterations 5.0736167E-02 1.228137 at 90iterations 2.6864305E-02 0.6718597 at 100iterations 1.4236145E-02 0.3525813 at 110iterations 7.5345989E-03 0.1956635 at 120iterations 3.9845901E-03 9.7621918E-02 at 130iterations 2.1041778E-03 4.8830509E-02 at 140iterations 1.1143868E-03 2.5444508E-02 at 150iterations 5.8783148E-04 1.4549494E-02 at 160iterations 3.1057917E-04 7.5817108E-03 at 170iterations 1.6474456E-04 3.7026405E-03 at 180iterations finished qdiffx linear iterations at : 14:04:31 total time elapsed so far: 16.76000 # loops : 180 mean,max change (kT/e) : 1.6474456E-04 3.7026405E-03 energy calculations done at 16.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.97000 DelPhi exited at 14:04:31 16.973u 0.486s 0:17.81 97.9% 0+0k 0+0io 0pf+0w