Mon Oct 10 12:26:38 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 Mon Oct 10 2011 at 12:26:38 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7527382 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): -22.21300 24.93800 ymin,ymax (A): -7.804000 38.29600 zmin,zma (A): -3.529000 43.76500 x,y,z range (A): 47.15100 46.10000 47.29400 scale (grids/A): 0.7527382 object centre (A): 1.362500 15.24600 20.11800 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 89.06716 89.65578 90.23662 assigned negative charge : -320.2120 centred at (gu) : 89.09399 89.70925 90.38682 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8167 nv = 96 ne = 84 npr = 44016 no. pairs analyzed = 44016 no. exposed pairs = 2684 no. arc points = 18862 no. surface atoms = 911 nbur = 1194 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 582 mr = 4540 m= 3 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.2500000 number of dielectric boundary points 4088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1481 ## 117 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8531 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5006504E-08 -3.2939701E-07 midg,1,midg; midg,igrid,midg -4.8260610E-08 -1.7469077E-07 1,midg,midg; igrid,midg,midg -9.4426703E-08 -1.2755724E-07 gauss-seidel spectral radius is 0.9907998 estimated iterations to convergence 85 setup time was (sec) 0.5200000 now iterating at: 12:26:38 rms-change max change #iterations 0.2618040 32.47203 at 10iterations 3.6854964E-02 4.665115 at 20iterations 5.1132604E-03 0.7109623 at 30iterations 7.1665697E-04 8.3396912E-02 at 40iterations 1.0036254E-04 1.3168335E-02 at 50iterations finished qdiffx linear iterations at : 12:26:42 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 1.0036254E-04 1.3168335E-02 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 12:26:43 4.131u 0.255s 0:04.96 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 12:26:43 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.258215 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): -22.21300 24.93800 ymin,ymax (A): -7.804000 38.29600 zmin,zma (A): -3.529000 43.76500 x,y,z range (A): 47.15100 46.10000 47.29400 scale (grids/A): 2.258215 object centre (A): 1.362500 15.24600 20.11800 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 87.20171 88.96729 90.70962 assigned negative charge : -320.2120 centred at (gu) : 87.28199 89.12775 91.16045 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85597 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18862 grid for indexing accessible points = 1.400000 m= 33891 mr = 58995 m= 7087 mr = 25667 m= 744 mr = 4858 m= 29 mr = 437 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1602 time to turn everything in is 0.6700000 number of dielectric boundary points 37382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 15686 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) : 0.7527382 object centre at (A) : 1.362500 15.24600 20.11800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7726339E-03 -0.1200144 midg,1,midg; midg,igrid,midg -2.7572481E-02 -3.9324228E-02 1,midg,midg; igrid,midg,midg -4.1460167E-03 1.8816288E-03 gauss-seidel spectral radius is 0.9989543 estimated iterations to convergence 245 setup time was (sec) 1.000000 now iterating at: 12:26:44 rms-change max change #iterations 5.222331 227.7791 at 10iterations 2.675173 89.69009 at 20iterations 1.378468 46.14397 at 30iterations 0.7083489 20.49345 at 40iterations 0.3647277 9.732034 at 50iterations 0.1875298 5.330004 at 60iterations 9.6400537E-02 2.639809 at 70iterations 4.9540840E-02 1.355820 at 80iterations 2.5467515E-02 0.6633997 at 90iterations 1.3131348E-02 0.3859291 at 100iterations 6.7434590E-03 0.1971912 at 110iterations 3.4731238E-03 8.7768078E-02 at 120iterations finished qdiffx linear iterations at : 12:26:52 total time elapsed so far: 9.570000 # loops : 120 mean,max change (kT/e) : 3.4731238E-03 8.7768078E-02 energy calculations done at 9.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.750000 DelPhi exited at 12:26:53 9.758u 0.249s 0:10.29 97.0% 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 12:26:53 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.387322 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): -22.21300 24.93800 ymin,ymax (A): -7.804000 38.29600 zmin,zma (A): -3.529000 43.76500 x,y,z range (A): 47.15100 46.10000 47.29400 scale (grids/A): 3.387322 object centre (A): 1.362500 15.24600 20.11800 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 85.80254 88.45084 91.06443 assigned negative charge : -320.2120 centred at (gu) : 85.92303 88.69168 91.74076 start vw surface at 0.1200000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 196823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18862 grid for indexing accessible points = 1.400000 m= 104261 mr = 142066 m= 44187 mr = 86215 m= 13834 mr = 36541 m= 3064 mr = 10913 m= 449 mr = 2401 m= 26 mr = 315 m= 0 mr = 18 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 5359 time to turn everything in is 2.160000 number of dielectric boundary points 84175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 15736 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) : 2.258215 object centre at (A) : 1.362500 15.24600 20.11800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9717647E-02 -1.135890 midg,1,midg; midg,igrid,midg -0.2543902 -0.1951577 1,midg,midg; igrid,midg,midg -2.0064704E-02 -2.8443113E-02 gauss-seidel spectral radius is 0.9993234 estimated iterations to convergence 303 setup time was (sec) 2.490000 now iterating at: 12:26:56 rms-change max change #iterations 11.15455 278.8008 at 10iterations 6.582781 136.3062 at 20iterations 3.893497 79.59818 at 30iterations 2.293711 39.54775 at 40iterations 1.354506 23.98664 at 50iterations 0.7946863 12.89882 at 60iterations 0.4688280 7.610464 at 70iterations 0.2764145 4.780949 at 80iterations 0.1625231 2.632957 at 90iterations 9.5590718E-02 1.546996 at 100iterations 5.6233276E-02 0.8696446 at 110iterations 3.3081621E-02 0.5333509 at 120iterations 1.9498590E-02 0.3230991 at 130iterations 1.1442342E-02 0.1948709 at 140iterations 6.7498293E-03 0.1102066 at 150iterations 3.9624446E-03 6.5646410E-02 at 160iterations 2.3324362E-03 3.5238266E-02 at 170iterations 1.3720747E-03 2.0977020E-02 at 180iterations finished qdiffx linear iterations at : 12:27:10 total time elapsed so far: 16.28000 # loops : 180 mean,max change (kT/e) : 1.3720747E-03 2.0977020E-02 energy calculations done at 16.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.46000 DelPhi exited at 12:27:10 16.460u 0.335s 0:17.23 97.4% 0+0k 0+0io 0pf+0w