Tue Oct 11 03:25:52 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 Tue Oct 11 2011 at 03:25:52 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3097 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: 0.5294704 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): -12.37300 38.91800 ymin,ymax (A): -27.43900 25.62100 zmin,zma (A): -19.98600 47.25100 x,y,z range (A): 51.29100 53.06000 67.23700 scale (grids/A): 0.5294704 object centre (A): 13.27250 -0.9089994 13.63250 number of atom coordinates read : 3097 total number of charged atoms : 2956 net assigned charge : 2.500021 assigned positive charge : 459.8118 centred at (gu) : 89.63410 90.28039 90.91404 assigned negative charge : -457.3132 centred at (gu) : 89.64417 90.32442 90.94955 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5704 nv = 96 ne = 84 npr = 60744 no. pairs analyzed = 60744 no. exposed pairs = 4517 no. arc points = 32171 no. surface atoms = 1499 nbur = 1598 mkacc time = 0.1300000 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= 213 mr = 2571 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3117 ## 417 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7489 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6613916E-10 -6.1130864E-11 midg,1,midg; midg,igrid,midg 2.2334470E-10 -8.4643952E-11 1,midg,midg; igrid,midg,midg 1.2933044E-10 4.1435230E-11 gauss-seidel spectral radius is 0.9816439 estimated iterations to convergence 61 setup time was (sec) 0.5500000 now iterating at: 03:25:53 rms-change max change #iterations 6.4509459E-02 12.38767 at 10iterations 4.1544386E-03 0.7594795 at 20iterations 4.0000808E-04 6.4241409E-02 at 30iterations 6.7220186E-05 1.1932373E-02 at 40iterations 1.3468315E-05 2.3651123E-03 at 50iterations finished qdiffx linear iterations at : 03:25:56 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.3468315E-05 2.3651123E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 03:25:56 3.137u 0.151s 0:03.66 89.6% 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 Tue Oct 11 2011 at 03:25:56 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3097 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: 1.588411 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): -12.37300 38.91800 ymin,ymax (A): -27.43900 25.62100 zmin,zma (A): -19.98600 47.25100 x,y,z range (A): 51.29100 53.06000 67.23700 scale (grids/A): 1.588411 object centre (A): 13.27250 -0.9089994 13.63250 number of atom coordinates read : 3097 total number of charged atoms : 2956 net assigned charge : 2.500021 assigned positive charge : 459.8118 centred at (gu) : 88.90186 90.84034 92.74127 assigned negative charge : -457.3132 centred at (gu) : 88.93190 90.97283 92.84826 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32171 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18189 mr = 39159 m= 1888 mr = 11537 m= 71 mr = 849 m= 3 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 31114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 22466 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) : 0.5294704 object centre at (A) : 13.27250 -0.9089994 13.63250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8254109E-03 -4.1162584E-04 midg,1,midg; midg,igrid,midg 4.6208533E-03 -3.1002392E-03 1,midg,midg; igrid,midg,midg 3.1288587E-03 8.6754039E-03 gauss-seidel spectral radius is 0.9981179 estimated iterations to convergence 183 setup time was (sec) 0.7900000 now iterating at: 03:25:57 rms-change max change #iterations 3.185492 150.5387 at 10iterations 1.294570 47.55578 at 20iterations 0.5287134 21.18095 at 30iterations 0.2169556 8.596581 at 40iterations 8.8638514E-02 3.060998 at 50iterations 3.6428533E-02 1.316559 at 60iterations 1.4943633E-02 0.5680618 at 70iterations 6.1510415E-03 0.2383804 at 80iterations 2.5298663E-03 0.1065788 at 90iterations 1.0466493E-03 4.2140007E-02 at 100iterations 4.3848171E-04 2.0080566E-02 at 110iterations 1.8643569E-04 7.5035095E-03 at 120iterations finished qdiffx linear iterations at : 03:26:03 total time elapsed so far: 6.990000 # loops : 120 mean,max change (kT/e) : 1.8643569E-04 7.5035095E-03 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.200000 DelPhi exited at 03:26:04 7.207u 0.225s 0:07.73 95.9% 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 Tue Oct 11 2011 at 03:26:04 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3097 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.382617 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): -12.37300 38.91800 ymin,ymax (A): -27.43900 25.62100 zmin,zma (A): -19.98600 47.25100 x,y,z range (A): 51.29100 53.06000 67.23700 scale (grids/A): 2.382617 object centre (A): 13.27250 -0.9089994 13.63250 number of atom coordinates read : 3097 total number of charged atoms : 2956 net assigned charge : 2.500021 assigned positive charge : 459.8118 centred at (gu) : 88.35242 91.26017 94.11164 assigned negative charge : -457.3132 centred at (gu) : 88.39768 91.45927 94.27232 start vw surface at 0.1700000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 145113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32171 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 62555 mr = 97087 m= 17738 mr = 46674 m= 2876 mr = 12601 m= 190 mr = 1685 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 70370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 23625 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) : 1.588411 object centre at (A) : 13.27250 -0.9089994 13.63250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1296532 -1.1988155E-02 midg,1,midg; midg,igrid,midg 8.4575653E-02 -9.3982190E-02 1,midg,midg; igrid,midg,midg 6.1357047E-02 0.2136910 gauss-seidel spectral radius is 0.9991335 estimated iterations to convergence 268 setup time was (sec) 1.440000 now iterating at: 03:26:06 rms-change max change #iterations 8.641596 258.5737 at 10iterations 4.929208 130.9411 at 20iterations 2.783259 66.12959 at 30iterations 1.567920 37.65303 at 40iterations 0.8723481 21.26379 at 50iterations 0.4858974 12.03586 at 60iterations 0.2687772 5.901188 at 70iterations 0.1490923 3.554786 at 80iterations 8.2170576E-02 1.768631 at 90iterations 4.5273330E-02 1.094814 at 100iterations 2.4888728E-02 0.5891218 at 110iterations 1.3696839E-02 0.2806931 at 120iterations 7.5313416E-03 0.1741295 at 130iterations 4.1407114E-03 8.4126472E-02 at 140iterations 2.2737067E-03 4.8682213E-02 at 150iterations 1.2498862E-03 2.7748108E-02 at 160iterations 6.8791863E-04 1.4774323E-02 at 170iterations 3.7925382E-04 8.3122253E-03 at 180iterations finished qdiffx linear iterations at : 03:26:16 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 3.7925382E-04 8.3122253E-03 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 03:26:17 12.326u 0.265s 0:12.93 97.2% 0+0k 0+0io 0pf+0w