Sat Oct 15 15:01:41 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 Sat Oct 15 2011 at 15:01:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 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: 0.5695726 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): 18.07700 80.58000 ymin,ymax (A): -11.49700 44.02000 zmin,zma (A): -7.938000 35.14100 x,y,z range (A): 62.50300 55.51700 43.07900 scale (grids/A): 0.5695726 object centre (A): 49.32850 16.26150 13.60150 number of atom coordinates read : 2629 total number of charged atoms : 2487 net assigned charge : 6.000024 assigned positive charge : 395.3988 centred at (gu) : 87.44476 89.76357 89.69010 assigned negative charge : -389.3995 centred at (gu) : 87.67782 89.89988 89.83949 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5547 nv = 96 ne = 84 npr = 53283 no. pairs analyzed = 53283 no. exposed pairs = 3077 no. arc points = 22006 no. surface atoms = 1041 nbur = 1588 mkacc time = 0.1500000 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 = 1.512000 m= 221 mr = 3024 m= 0 mr = 15 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3300000 number of dielectric boundary points 2729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7144 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9952194E-09 -1.1527000E-09 midg,1,midg; midg,igrid,midg 2.7627707E-09 -1.0018184E-09 1,midg,midg; igrid,midg,midg 7.1821478E-09 -1.3029970E-09 gauss-seidel spectral radius is 0.9840626 estimated iterations to convergence 65 setup time was (sec) 0.6000000 now iterating at: 15:01:42 rms-change max change #iterations 8.6711764E-02 17.09622 at 10iterations 7.3018288E-03 1.555050 at 20iterations 9.4238680E-04 0.2388954 at 30iterations 2.0477352E-04 5.5774689E-02 at 40iterations 4.7455393E-05 1.3179779E-02 at 50iterations finished qdiffx linear iterations at : 15:01:46 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 4.7455393E-05 1.3179779E-02 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 15:01:46 4.160u 0.319s 0:04.76 93.9% 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 15 2011 at 15:01:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 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: 1.708718 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): 18.07700 80.58000 ymin,ymax (A): -11.49700 44.02000 zmin,zma (A): -7.938000 35.14100 x,y,z range (A): 62.50300 55.51700 43.07900 scale (grids/A): 1.708718 object centre (A): 49.32850 16.26150 13.60150 number of atom coordinates read : 2629 total number of charged atoms : 2487 net assigned charge : 6.000024 assigned positive charge : 395.3988 centred at (gu) : 82.33385 89.28984 89.06978 assigned negative charge : -389.3995 centred at (gu) : 83.03312 89.69926 89.51825 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 61582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22006 grid for indexing accessible points = 1.400000 m= 19342 mr = 42972 m= 2213 mr = 13784 m= 65 mr = 1208 m= 0 mr = 9 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2301 time to turn everything in is 0.5500000 number of dielectric boundary points 25229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19264 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) : 0.5695726 object centre at (A) : 49.32850 16.26150 13.60150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5943367E-02 1.0488678E-03 midg,1,midg; midg,igrid,midg 1.8434539E-02 -1.9941850E-02 1,midg,midg; igrid,midg,midg 7.3196352E-03 2.8631524E-03 gauss-seidel spectral radius is 0.9983023 estimated iterations to convergence 193 setup time was (sec) 0.8600000 now iterating at: 15:01:47 rms-change max change #iterations 3.386660 156.5793 at 10iterations 1.446694 52.81818 at 20iterations 0.6225789 22.60441 at 30iterations 0.2660192 10.17398 at 40iterations 0.1147900 4.717819 at 50iterations 4.9704980E-02 1.782764 at 60iterations 2.1435184E-02 0.7345867 at 70iterations 9.3407435E-03 0.3486404 at 80iterations 4.1131494E-03 0.1663818 at 90iterations 1.8837284E-03 8.2683563E-02 at 100iterations 9.0933603E-04 3.9110184E-02 at 110iterations 4.6054387E-04 2.1350861E-02 at 120iterations finished qdiffx linear iterations at : 15:01:56 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 4.6054387E-04 2.1350861E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 15:01:56 9.441u 0.320s 0:10.05 97.1% 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 15 2011 at 15:01:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 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: 2.563077 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): 18.07700 80.58000 ymin,ymax (A): -11.49700 44.02000 zmin,zma (A): -7.938000 35.14100 x,y,z range (A): 62.50300 55.51700 43.07900 scale (grids/A): 2.563077 object centre (A): 49.32850 16.26150 13.60150 number of atom coordinates read : 2629 total number of charged atoms : 2487 net assigned charge : 6.000024 assigned positive charge : 395.3988 centred at (gu) : 78.50069 88.93469 88.60455 assigned negative charge : -389.3995 centred at (gu) : 79.54968 89.54887 89.27744 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 143134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22006 grid for indexing accessible points = 1.400000 m= 66994 mr = 104570 m= 19841 mr = 54253 m= 3565 mr = 15397 m= 258 mr = 2505 m= 3 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.7699999 no. cavity mid-points inaccessible to solvent = 7733 time to turn everything in is 1.340000 number of dielectric boundary points 56949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 19884 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) : 1.708718 object centre at (A) : 49.32850 16.26150 13.60150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1811904 2.1275543E-02 midg,1,midg; midg,igrid,midg 0.2314554 -0.4360741 1,midg,midg; igrid,midg,midg -5.8990512E-03 0.1780220 gauss-seidel spectral radius is 0.9991592 estimated iterations to convergence 272 setup time was (sec) 1.650000 now iterating at: 15:01:58 rms-change max change #iterations 8.381151 264.5690 at 10iterations 4.640587 114.7232 at 20iterations 2.585117 60.68346 at 30iterations 1.431967 32.16740 at 40iterations 0.7939634 17.49006 at 50iterations 0.4406486 9.654611 at 60iterations 0.2436638 5.327583 at 70iterations 0.1348857 2.639624 at 80iterations 7.4752569E-02 1.609737 at 90iterations 4.1461267E-02 0.8601475 at 100iterations 2.2980535E-02 0.5449219 at 110iterations 1.2828959E-02 0.2751484 at 120iterations 7.2128759E-03 0.1475220 at 130iterations 4.0990491E-03 9.1373444E-02 at 140iterations 2.3669309E-03 6.0646057E-02 at 150iterations 1.4204473E-03 3.9054871E-02 at 160iterations 8.8354712E-04 2.4349213E-02 at 170iterations 5.7580555E-04 1.6170502E-02 at 180iterations finished qdiffx linear iterations at : 15:02:12 total time elapsed so far: 15.24000 # loops : 180 mean,max change (kT/e) : 5.7580555E-04 1.6170502E-02 energy calculations done at 15.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.42000 DelPhi exited at 15:02:12 15.424u 0.347s 0:16.13 97.7% 0+0k 0+0io 0pf+0w