Mon Oct 10 17:01:14 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 17:01:14 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6134970 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): 13.62100 71.14000 ymin,ymax (A): 3.916000 51.00600 zmin,zma (A): 7.791000 65.81900 x,y,z range (A): 57.51900 47.09000 58.02800 scale (grids/A): 0.6134970 object centre (A): 42.38050 27.46100 36.80500 number of atom coordinates read : 3013 total number of charged atoms : 2868 net assigned charge : -2.499966 assigned positive charge : 452.8399 centred at (gu) : 89.29089 90.34785 90.39487 assigned negative charge : -455.3411 centred at (gu) : 89.15344 90.43567 90.51027 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7621 nv = 96 ne = 84 npr = 59922 no. pairs analyzed = 59922 no. exposed pairs = 3909 no. arc points = 27719 no. surface atoms = 1325 nbur = 1688 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3980 m= 0 mr = 31 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2766 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9406 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3247069E-09 -9.8781481E-09 midg,1,midg; midg,igrid,midg 3.7771981E-09 -7.8060465E-09 1,midg,midg; igrid,midg,midg -1.2324155E-08 6.1321823E-09 gauss-seidel spectral radius is 0.9862863 estimated iterations to convergence 70 setup time was (sec) 0.5800000 now iterating at: 17:01:15 rms-change max change #iterations 0.1265800 19.00402 at 10iterations 1.1397996E-02 1.574281 at 20iterations 1.0053694E-03 0.1433907 at 30iterations 9.3977811E-05 1.4755249E-02 at 40iterations 8.8939942E-06 1.5792847E-03 at 50iterations finished qdiffx linear iterations at : 17:01:17 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 8.8939942E-06 1.5792847E-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) 3.370000 DelPhi exited at 17:01:18 3.373u 0.196s 0:04.03 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 17:01:18 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 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: 1.840491 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): 13.62100 71.14000 ymin,ymax (A): 3.916000 51.00600 zmin,zma (A): 7.791000 65.81900 x,y,z range (A): 57.51900 47.09000 58.02800 scale (grids/A): 1.840491 object centre (A): 42.38050 27.46100 36.80500 number of atom coordinates read : 3013 total number of charged atoms : 2868 net assigned charge : -2.499966 assigned positive charge : 452.8399 centred at (gu) : 87.87211 91.04256 91.18367 assigned negative charge : -455.3411 centred at (gu) : 87.46004 91.30671 91.53044 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27719 grid for indexing accessible points = 1.400000 m= 27304 mr = 56210 m= 3712 mr = 19224 m= 173 mr = 2044 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 938 time to turn everything in is 0.5900000 number of dielectric boundary points 36537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 22479 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) : 0.6134970 object centre at (A) : 42.38050 27.46100 36.80500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2228025E-02 -4.7457108E-04 midg,1,midg; midg,igrid,midg 6.8001420E-04 -1.9416422E-02 1,midg,midg; igrid,midg,midg -3.5510249E-02 2.9279940E-02 gauss-seidel spectral radius is 0.9985917 estimated iterations to convergence 211 setup time was (sec) 0.8900000 now iterating at: 17:01:19 rms-change max change #iterations 4.307279 190.0976 at 10iterations 1.984244 64.92959 at 20iterations 0.9128629 29.30896 at 30iterations 0.4229053 14.08640 at 40iterations 0.1952609 5.426466 at 50iterations 9.0289868E-02 2.811501 at 60iterations 4.1747823E-02 1.357367 at 70iterations 1.9321300E-02 0.6231775 at 80iterations 8.9273797E-03 0.2711487 at 90iterations 4.1379426E-03 0.1259314 at 100iterations 1.9110963E-03 5.8813095E-02 at 110iterations 8.8420714E-04 2.6983261E-02 at 120iterations finished qdiffx linear iterations at : 17:01:27 total time elapsed so far: 8.730000 # loops : 120 mean,max change (kT/e) : 8.8420714E-04 2.6983261E-02 energy calculations done at 8.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.900000 DelPhi exited at 17:01:28 8.899u 0.264s 0:09.69 94.4% 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 17:01:28 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 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: 2.760736 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): 13.62100 71.14000 ymin,ymax (A): 3.916000 51.00600 zmin,zma (A): 7.791000 65.81900 x,y,z range (A): 57.51900 47.09000 58.02800 scale (grids/A): 2.760736 object centre (A): 42.38050 27.46100 36.80500 number of atom coordinates read : 3013 total number of charged atoms : 2868 net assigned charge : -2.499966 assigned positive charge : 452.8399 centred at (gu) : 86.80808 91.56372 91.77529 assigned negative charge : -455.3411 centred at (gu) : 86.19000 91.95988 92.29551 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 192114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27719 grid for indexing accessible points = 1.400000 m= 91205 mr = 137074 m= 29970 mr = 72854 m= 6197 mr = 23027 m= 678 mr = 4254 m= 26 mr = 414 m= 0 mr = 10 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 3022 time to turn everything in is 1.380000 number of dielectric boundary points 82557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 22942 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) : 1.840491 object centre at (A) : 42.38050 27.46100 36.80500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2345612 0.2104045 midg,1,midg; midg,igrid,midg -1.0514617E-02 -0.1631336 1,midg,midg; igrid,midg,midg -0.4181817 0.4225785 gauss-seidel spectral radius is 0.9992661 estimated iterations to convergence 291 setup time was (sec) 1.670000 now iterating at: 17:01:29 rms-change max change #iterations 10.36071 330.3838 at 10iterations 6.116695 147.0934 at 20iterations 3.580215 77.82880 at 30iterations 2.081104 45.82055 at 40iterations 1.210089 22.77850 at 50iterations 0.7010458 13.61120 at 60iterations 0.4057220 9.237064 at 70iterations 0.2341629 4.680326 at 80iterations 0.1353491 2.618608 at 90iterations 7.8085423E-02 1.423999 at 100iterations 4.5075651E-02 0.7704239 at 110iterations 2.6014416E-02 0.4672737 at 120iterations 1.4966870E-02 0.2817688 at 130iterations 8.6235134E-03 0.1535358 at 140iterations 4.9695182E-03 8.5769892E-02 at 150iterations 2.8661480E-03 5.4183006E-02 at 160iterations 1.6493602E-03 2.8978348E-02 at 170iterations 9.5039612E-04 1.8253326E-02 at 180iterations finished qdiffx linear iterations at : 17:01:39 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 9.5039612E-04 1.8253326E-02 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.34000 DelPhi exited at 17:01:40 11.338u 0.182s 0:12.60 91.3% 0+0k 0+0io 0pf+0w