Sat Oct 8 11:39:28 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 Sat Oct 8 2011 at 11:39:28 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5770789 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): -4.606000 39.08700 ymin,ymax (A): 21.70700 83.39700 zmin,zma (A): 26.43200 81.79601 x,y,z range (A): 43.69300 61.69000 55.36401 scale (grids/A): 0.5770789 object centre (A): 17.24050 52.55200 54.11400 number of atom coordinates read : 2619 total number of charged atoms : 2469 net assigned charge : 1.000007 assigned positive charge : 389.2936 centred at (gu) : 90.67363 90.35836 89.87723 assigned negative charge : -388.2943 centred at (gu) : 90.62031 90.22070 89.93296 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5660 nv = 96 ne = 84 npr = 52843 no. pairs analyzed = 52843 no. exposed pairs = 3371 no. arc points = 23418 no. surface atoms = 1145 nbur = 1474 mkacc time = 0.1400000 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= 284 mr = 2925 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2313 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1818203E-09 -7.7438050E-10 midg,1,midg; midg,igrid,midg -2.0746596E-09 2.7726847E-09 1,midg,midg; igrid,midg,midg -6.4162159E-10 1.2990502E-09 gauss-seidel spectral radius is 0.9844746 estimated iterations to convergence 66 setup time was (sec) 0.7900000 now iterating at: 11:39:30 rms-change max change #iterations 9.1480277E-02 19.35206 at 10iterations 7.0691579E-03 1.172487 at 20iterations 5.8050698E-04 8.4604263E-02 at 30iterations 8.1329061E-05 1.7835617E-02 at 40iterations 2.4775582E-05 5.9804916E-03 at 50iterations finished qdiffx linear iterations at : 11:39:36 total time elapsed so far: 7.130000 # loops : 50 mean,max change (kT/e) : 2.4775582E-05 5.9804916E-03 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 11:39:37 7.309u 0.596s 0:08.37 94.2% 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 Sat Oct 8 2011 at 11:39:37 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.731237 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): -4.606000 39.08700 ymin,ymax (A): 21.70700 83.39700 zmin,zma (A): 26.43200 81.79601 x,y,z range (A): 43.69300 61.69000 55.36401 scale (grids/A): 1.731237 object centre (A): 17.24050 52.55200 54.11400 number of atom coordinates read : 2619 total number of charged atoms : 2469 net assigned charge : 1.000007 assigned positive charge : 389.2936 centred at (gu) : 92.02029 91.07441 89.63074 assigned negative charge : -388.2943 centred at (gu) : 91.86045 90.66175 89.79871 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23418 grid for indexing accessible points = 1.400000 m= 19136 mr = 41631 m= 2418 mr = 13192 m= 88 mr = 1314 m= 1 mr = 13 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 0.6100000 number of dielectric boundary points 27704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19152 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) : 0.5770789 object centre at (A) : 17.24050 52.55200 54.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6110691E-04 -1.6725784E-02 midg,1,midg; midg,igrid,midg 9.6162846E-03 2.1005914E-02 1,midg,midg; igrid,midg,midg -4.3640751E-04 4.7688219E-03 gauss-seidel spectral radius is 0.9983534 estimated iterations to convergence 196 setup time was (sec) 1.100000 now iterating at: 11:39:39 rms-change max change #iterations 3.521794 163.1814 at 10iterations 1.522493 74.68089 at 20iterations 0.6574490 27.73672 at 30iterations 0.2857599 10.24757 at 40iterations 0.1241744 4.315873 at 50iterations 5.3952433E-02 2.001083 at 60iterations 2.3562633E-02 0.7967491 at 70iterations 1.0237132E-02 0.3769608 at 80iterations 4.4703614E-03 0.1737428 at 90iterations 1.9695959E-03 6.4963579E-02 at 100iterations 8.8824815E-04 4.5038700E-02 at 110iterations 4.2362118E-04 1.6578674E-02 at 120iterations finished qdiffx linear iterations at : 11:39:55 total time elapsed so far: 17.69000 # loops : 120 mean,max change (kT/e) : 4.2362118E-04 1.6578674E-02 energy calculations done at 17.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.87000 DelPhi exited at 11:39:56 17.877u 0.705s 0:18.93 98.0% 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 Sat Oct 8 2011 at 11:39:56 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.596855 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): -4.606000 39.08700 ymin,ymax (A): 21.70700 83.39700 zmin,zma (A): 26.43200 81.79601 x,y,z range (A): 43.69300 61.69000 55.36401 scale (grids/A): 2.596855 object centre (A): 17.24050 52.55200 54.11400 number of atom coordinates read : 2619 total number of charged atoms : 2469 net assigned charge : 1.000007 assigned positive charge : 389.2936 centred at (gu) : 93.03008 91.61148 89.44604 assigned negative charge : -388.2943 centred at (gu) : 92.79060 90.99258 89.69799 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 144199 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23418 grid for indexing accessible points = 1.400000 m= 65383 mr = 101746 m= 19917 mr = 51606 m= 4003 mr = 15100 m= 388 mr = 2775 m= 11 mr = 198 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 62476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 19747 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) : 1.731237 object centre at (A) : 17.24050 52.55200 54.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2562396E-02 -0.2057907 midg,1,midg; midg,igrid,midg 0.2429824 0.2854121 1,midg,midg; igrid,midg,midg 1.2289752E-03 4.5474924E-02 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.990000 now iterating at: 11:39:59 rms-change max change #iterations 8.701074 278.6557 at 10iterations 4.935033 121.8463 at 20iterations 2.788803 64.00851 at 30iterations 1.569200 39.20530 at 40iterations 0.8805178 22.71518 at 50iterations 0.4945975 11.37071 at 60iterations 0.2764708 6.146064 at 70iterations 0.1550793 3.345966 at 80iterations 8.6623877E-02 1.974461 at 90iterations 4.8380211E-02 0.9775543 at 100iterations 2.7083036E-02 0.5907707 at 110iterations 1.5128653E-02 0.4017830 at 120iterations 8.4721074E-03 0.1828349 at 130iterations 4.7668107E-03 0.1128016 at 140iterations 2.7010089E-03 6.3383102E-02 at 150iterations 1.5612532E-03 3.7321091E-02 at 160iterations 9.3135680E-04 2.7306795E-02 at 170iterations 5.8741274E-04 1.5006065E-02 at 180iterations finished qdiffx linear iterations at : 11:40:25 total time elapsed so far: 28.13000 # loops : 180 mean,max change (kT/e) : 5.8741274E-04 1.5006065E-02 energy calculations done at 28.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.32000 DelPhi exited at 11:40:25 28.329u 0.798s 0:29.44 98.8% 0+0k 0+0io 0pf+0w