Sun Oct 9 11:15:36 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 Sun Oct 9 2011 at 11:15:36 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: HIR 212 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5842866 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): -19.88200 41.04700 ymin,ymax (A): -29.14400 29.87700 zmin,zma (A): 1.352000 55.90200 x,y,z range (A): 60.92900 59.02100 54.55000 scale (grids/A): 0.5842866 object centre (A): 10.58250 0.3665009 28.62700 number of atom coordinates read : 2869 total number of charged atoms : 2798 net assigned charge : 6.514018 assigned positive charge : 433.1530 centred at (gu) : 90.58084 91.02680 88.98885 assigned negative charge : -426.6408 centred at (gu) : 90.57913 91.04031 89.06548 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6828 nv = 96 ne = 84 npr = 54055 no. pairs analyzed = 54055 no. exposed pairs = 4131 no. arc points = 29226 no. surface atoms = 1368 nbur = 1501 mkacc time = 0.1100000 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 = 1.484000 m= 354 mr = 3372 m= 4 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2891 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3945865E-09 -1.8000407E-10 midg,1,midg; midg,igrid,midg 1.5522540E-09 1.6362721E-09 1,midg,midg; igrid,midg,midg 1.3943332E-09 1.9054061E-09 gauss-seidel spectral radius is 0.9848883 estimated iterations to convergence 67 setup time was (sec) 0.5300000 now iterating at: 11:15:37 rms-change max change #iterations 9.7602621E-02 16.39002 at 10iterations 7.7968840E-03 1.168671 at 20iterations 7.0378202E-04 9.5075607E-02 at 30iterations 1.0375884E-04 1.4963150E-02 at 40iterations 2.3451992E-05 3.1547546E-03 at 50iterations finished qdiffx linear iterations at : 11:15:39 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.3451992E-05 3.1547546E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 11:15:40 3.345u 0.210s 0:03.87 91.7% 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 11:15:40 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: HIR 212 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.752860 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): -19.88200 41.04700 ymin,ymax (A): -29.14400 29.87700 zmin,zma (A): 1.352000 55.90200 x,y,z range (A): 60.92900 59.02100 54.55000 scale (grids/A): 1.752860 object centre (A): 10.58250 0.3665009 28.62700 number of atom coordinates read : 2869 total number of charged atoms : 2798 net assigned charge : 6.514018 assigned positive charge : 433.1530 centred at (gu) : 91.74152 93.07947 86.96553 assigned negative charge : -426.6408 centred at (gu) : 91.73738 93.12112 87.19643 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29226 grid for indexing accessible points = 1.400000 m= 24424 mr = 49031 m= 3350 mr = 16462 m= 129 mr = 1781 m= 0 mr = 13 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.5300000 number of dielectric boundary points 35135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21824 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) : 0.5842866 object centre at (A) : 10.58250 0.3665009 28.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2695826E-02 -5.0057997E-03 midg,1,midg; midg,igrid,midg 2.2984395E-02 2.8448697E-02 1,midg,midg; igrid,midg,midg -6.1449301E-03 1.6604647E-02 gauss-seidel spectral radius is 0.9984503 estimated iterations to convergence 202 setup time was (sec) 0.8200000 now iterating at: 11:15:41 rms-change max change #iterations 3.804300 179.0421 at 10iterations 1.684119 63.14029 at 20iterations 0.7484996 26.89571 at 30iterations 0.3331535 11.42362 at 40iterations 0.1482925 4.828678 at 50iterations 6.6124558E-02 2.175217 at 60iterations 2.9350413E-02 1.186462 at 70iterations 1.3091685E-02 0.4506950 at 80iterations 5.8302293E-03 0.2341014 at 90iterations 2.6156483E-03 9.6251488E-02 at 100iterations 1.1748207E-03 4.0449142E-02 at 110iterations 5.3089077E-04 1.6574860E-02 at 120iterations finished qdiffx linear iterations at : 11:15:48 total time elapsed so far: 8.190000 # loops : 120 mean,max change (kT/e) : 5.3089077E-04 1.6574860E-02 energy calculations done at 8.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.360000 DelPhi exited at 11:15:49 8.364u 0.226s 0:08.98 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 Sun Oct 9 2011 at 11:15:49 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: HIR 212 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.629290 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): -19.88200 41.04700 ymin,ymax (A): -29.14400 29.87700 zmin,zma (A): 1.352000 55.90200 x,y,z range (A): 60.92900 59.02100 54.55000 scale (grids/A): 2.629290 object centre (A): 10.58250 0.3665009 28.62700 number of atom coordinates read : 2869 total number of charged atoms : 2798 net assigned charge : 6.514018 assigned positive charge : 433.1530 centred at (gu) : 92.61217 94.61900 85.44814 assigned negative charge : -426.6408 centred at (gu) : 92.60598 94.68166 85.79470 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 172943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29226 grid for indexing accessible points = 1.400000 m= 80719 mr = 120656 m= 26627 mr = 62457 m= 5753 mr = 20025 m= 569 mr = 3937 m= 12 mr = 298 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 708 time to turn everything in is 1.270000 number of dielectric boundary points 79250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 22373 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) : 1.752860 object centre at (A) : 10.58250 0.3665009 28.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1489121 -5.3518903E-02 midg,1,midg; midg,igrid,midg 0.2840170 0.4100550 1,midg,midg; igrid,midg,midg -0.1478458 0.3461794 gauss-seidel spectral radius is 0.9992274 estimated iterations to convergence 284 setup time was (sec) 1.600000 now iterating at: 11:15:51 rms-change max change #iterations 9.572660 308.3511 at 10iterations 5.625720 135.3795 at 20iterations 3.278388 74.80061 at 30iterations 1.894473 39.09121 at 40iterations 1.095116 25.06746 at 50iterations 0.6292741 12.59674 at 60iterations 0.3602727 7.013055 at 70iterations 0.2060906 4.480852 at 80iterations 0.1177714 2.259721 at 90iterations 6.7237481E-02 1.344273 at 100iterations 3.8239501E-02 0.7672720 at 110iterations 2.1744082E-02 0.4213390 at 120iterations 1.2388202E-02 0.2587929 at 130iterations 7.0542055E-03 0.1521428 at 140iterations 4.0238914E-03 8.1077576E-02 at 150iterations 2.2965677E-03 4.7725677E-02 at 160iterations 1.3105109E-03 2.6268959E-02 at 170iterations 7.5208215E-04 1.4709473E-02 at 180iterations finished qdiffx linear iterations at : 11:16:01 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 7.5208215E-04 1.4709473E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 11:16:02 12.237u 0.243s 0:12.83 97.1% 0+0k 0+0io 0pf+0w