Mon Oct 10 16:13:45 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 16:13:45 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 = 4804 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5328224 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): -20.32700 46.48700 ymin,ymax (A): 8.122000 73.10600 zmin,zma (A): 32.96200 95.72701 x,y,z range (A): 66.81400 64.98399 62.76501 scale (grids/A): 0.5328224 object centre (A): 13.08000 40.61400 64.34450 number of atom coordinates read : 4804 total number of charged atoms : 4644 net assigned charge : 2.000013 assigned positive charge : 722.2144 centred at (gu) : 90.48673 90.86330 89.88090 assigned negative charge : -720.2191 centred at (gu) : 90.45612 90.80849 89.88390 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8694 nv = 96 ne = 84 npr = 98188 no. pairs analyzed = 98188 no. exposed pairs = 5805 no. arc points = 39498 no. surface atoms = 1939 nbur = 2865 mkacc time = 0.3300000 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 = 1.596000 m= 357 mr = 4781 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 4254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3984 ## 527 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 11665 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1028629E-11 4.7915723E-11 midg,1,midg; midg,igrid,midg -2.3186009E-10 5.2758747E-10 1,midg,midg; igrid,midg,midg -1.1519202E-10 3.0236727E-10 gauss-seidel spectral radius is 0.9819807 estimated iterations to convergence 61 setup time was (sec) 0.9900000 now iterating at: 16:13:46 rms-change max change #iterations 8.3819039E-02 12.00141 at 10iterations 6.2542381E-03 0.8340378 at 20iterations 1.1998976E-03 0.1845398 at 30iterations 4.5161578E-04 5.9806824E-02 at 40iterations 1.8674415E-04 2.1862030E-02 at 50iterations finished qdiffx linear iterations at : 16:13:50 total time elapsed so far: 4.900000 # loops : 50 mean,max change (kT/e) : 1.8674415E-04 2.1862030E-02 energy calculations done at 4.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 16:13:51 5.134u 0.454s 0:05.88 94.8% 0+0k 0+0io 5pf+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 16:13:51 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 = 4804 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.598467 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): -20.32700 46.48700 ymin,ymax (A): 8.122000 73.10600 zmin,zma (A): 32.96200 95.72701 x,y,z range (A): 66.81400 64.98399 62.76501 scale (grids/A): 1.598467 object centre (A): 13.08000 40.61400 64.34450 number of atom coordinates read : 4804 total number of charged atoms : 4644 net assigned charge : 2.000013 assigned positive charge : 722.2144 centred at (gu) : 91.45864 92.58830 89.64095 assigned negative charge : -720.2191 centred at (gu) : 91.36800 92.42497 89.65128 start vw surface at 0.2300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 98577 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 31594 mr = 70028 m= 3328 mr = 22193 m= 74 mr = 1674 m= 0 mr = 5 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 825 time to turn everything in is 1.030000 number of dielectric boundary points 39673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 428 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 35375 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) : 0.5328224 object centre at (A) : 13.08000 40.61400 64.34450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5890072E-03 1.2743548E-02 midg,1,midg; midg,igrid,midg -7.8028440E-03 -1.0840626E-03 1,midg,midg; igrid,midg,midg -3.0978503E-02 8.5294517E-03 gauss-seidel spectral radius is 0.9982868 estimated iterations to convergence 192 setup time was (sec) 1.380000 now iterating at: 16:13:53 rms-change max change #iterations 4.177841 191.9153 at 10iterations 1.785769 65.41241 at 20iterations 0.7625505 22.05031 at 30iterations 0.3263687 9.805879 at 40iterations 0.1401322 4.148232 at 50iterations 6.0090087E-02 1.803545 at 60iterations 2.5956189E-02 0.7898421 at 70iterations 1.1262669E-02 0.3248558 at 80iterations 5.0301026E-03 0.1634278 at 90iterations 2.3630685E-03 8.5798264E-02 at 100iterations 1.2239509E-03 3.7372589E-02 at 110iterations 7.2874333E-04 1.9962311E-02 at 120iterations finished qdiffx linear iterations at : 16:14:03 total time elapsed so far: 11.41000 # loops : 120 mean,max change (kT/e) : 7.2874333E-04 1.9962311E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 16:14:03 11.632u 0.504s 0:12.42 97.6% 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 16:14:03 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 = 4804 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.397701 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): -20.32700 46.48700 ymin,ymax (A): 8.122000 73.10600 zmin,zma (A): 32.96200 95.72701 x,y,z range (A): 66.81400 64.98399 62.76501 scale (grids/A): 2.397701 object centre (A): 13.08000 40.61400 64.34450 number of atom coordinates read : 4804 total number of charged atoms : 4644 net assigned charge : 2.000013 assigned positive charge : 722.2144 centred at (gu) : 92.18750 93.88207 89.46095 assigned negative charge : -720.2191 centred at (gu) : 92.05196 93.63735 89.47681 start vw surface at 0.2200000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 229814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 109589 mr = 171624 m= 31918 mr = 87575 m= 5159 mr = 24394 m= 316 mr = 3475 m= 1 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 1.570000 no. cavity mid-points inaccessible to solvent = 2750 time to turn everything in is 2.530000 number of dielectric boundary points 89588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 2.790000 number of grid points assigned charge 37082 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) : 1.598467 object centre at (A) : 13.08000 40.61400 64.34450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1967355E-02 0.1894254 midg,1,midg; midg,igrid,midg -0.1437569 -1.4183604E-02 1,midg,midg; igrid,midg,midg -0.6092335 0.1602472 gauss-seidel spectral radius is 0.9992098 estimated iterations to convergence 281 setup time was (sec) 3.010000 now iterating at: 16:14:07 rms-change max change #iterations 10.96022 351.0473 at 10iterations 6.387590 129.3391 at 20iterations 3.703300 76.05189 at 30iterations 2.137546 43.21841 at 40iterations 1.224878 25.37403 at 50iterations 0.7005110 13.73550 at 60iterations 0.4000800 7.631071 at 70iterations 0.2283302 4.346637 at 80iterations 0.1298859 2.540626 at 90iterations 7.3885851E-02 1.311919 at 100iterations 4.2024035E-02 0.8819666 at 110iterations 2.3914352E-02 0.4712639 at 120iterations 1.3687422E-02 0.2425900 at 130iterations 7.8800227E-03 0.1373625 at 140iterations 4.6103876E-03 8.2765579E-02 at 150iterations 2.7745164E-03 5.2469254E-02 at 160iterations 1.7531245E-03 3.2857895E-02 at 170iterations 1.1758464E-03 1.9709349E-02 at 180iterations finished qdiffx linear iterations at : 16:14:24 total time elapsed so far: 20.20000 # loops : 180 mean,max change (kT/e) : 1.1758464E-03 1.9709349E-02 energy calculations done at 20.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.41000 DelPhi exited at 16:14:25 20.417u 0.557s 0:21.31 98.3% 0+0k 0+0io 0pf+0w