Tue Oct 11 06:56:36 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 06:56:36 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 = 2976 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: 0.5448090 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): -20.70400 44.64000 ymin,ymax (A): 21.75800 77.83500 zmin,zma (A): -71.08801 -22.81600 x,y,z range (A): 65.34400 56.07700 48.27200 scale (grids/A): 0.5448090 object centre (A): 11.96800 49.79650 -46.95200 number of atom coordinates read : 2976 total number of charged atoms : 2835 net assigned charge : -1.999988 assigned positive charge : 433.9566 centred at (gu) : 89.69098 89.92526 89.60170 assigned negative charge : -435.9572 centred at (gu) : 89.66062 90.03188 89.57854 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5690 nv = 96 ne = 84 npr = 62084 no. pairs analyzed = 62084 no. exposed pairs = 3642 no. arc points = 25628 no. surface atoms = 1235 nbur = 1741 mkacc time = 0.1800000 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 = 1.568000 m= 216 mr = 3018 m= 0 mr = 14 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 2874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2586 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7475 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9001693E-10 2.3247890E-11 midg,1,midg; midg,igrid,midg 5.4904131E-10 -7.7756646E-10 1,midg,midg; igrid,midg,midg -3.3259462E-10 6.5194045E-11 gauss-seidel spectral radius is 0.9826310 estimated iterations to convergence 63 setup time was (sec) 0.6500000 now iterating at: 06:56:37 rms-change max change #iterations 7.2315261E-02 11.95018 at 10iterations 4.9854452E-03 0.7723598 at 20iterations 3.5096944E-04 5.7746887E-02 at 30iterations 3.6750022E-05 8.2786083E-03 at 40iterations 6.2036315E-06 1.5296936E-03 at 50iterations finished qdiffx linear iterations at : 06:56:41 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 6.2036315E-06 1.5296936E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 06:56:41 4.119u 0.268s 0:04.68 93.3% 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 Tue Oct 11 2011 at 06:56:41 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 = 2976 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: 1.634427 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): -20.70400 44.64000 ymin,ymax (A): 21.75800 77.83500 zmin,zma (A): -71.08801 -22.81600 x,y,z range (A): 65.34400 56.07700 48.27200 scale (grids/A): 1.634427 object centre (A): 11.96800 49.79650 -46.95200 number of atom coordinates read : 2976 total number of charged atoms : 2835 net assigned charge : -1.999988 assigned positive charge : 433.9566 centred at (gu) : 89.07204 89.77520 88.80449 assigned negative charge : -435.9572 centred at (gu) : 88.98157 90.09542 88.73533 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 63005 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25628 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19704 mr = 42917 m= 2113 mr = 13975 m= 39 mr = 1114 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 224 time to turn everything in is 0.5800000 number of dielectric boundary points 26849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 21714 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) : 0.5448090 object centre at (A) : 11.96800 49.79650 -46.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7225605E-03 8.2581360E-03 midg,1,midg; midg,igrid,midg -3.1886525E-03 3.4483941E-03 1,midg,midg; igrid,midg,midg -1.0238018E-02 -2.0505447E-02 gauss-seidel spectral radius is 0.9981892 estimated iterations to convergence 187 setup time was (sec) 0.8600000 now iterating at: 06:56:42 rms-change max change #iterations 3.277245 147.7388 at 10iterations 1.369024 54.65176 at 20iterations 0.5706895 21.86755 at 30iterations 0.2393748 9.118925 at 40iterations 0.1000102 4.020691 at 50iterations 4.1776080E-02 1.551386 at 60iterations 1.7425368E-02 0.5924702 at 70iterations 7.2879884E-03 0.2654862 at 80iterations 3.0418774E-03 0.1127243 at 90iterations 1.2746415E-03 5.5821419E-02 at 100iterations 5.3252396E-04 2.2844315E-02 at 110iterations 2.2268183E-04 7.9269409E-03 at 120iterations finished qdiffx linear iterations at : 06:56:50 total time elapsed so far: 9.020000 # loops : 120 mean,max change (kT/e) : 2.2268183E-04 7.9269409E-03 energy calculations done at 9.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.200000 DelPhi exited at 06:56:51 9.201u 0.310s 0:10.11 94.0% 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 Tue Oct 11 2011 at 06:56:51 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 = 2976 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: 2.451640 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): -20.70400 44.64000 ymin,ymax (A): 21.75800 77.83500 zmin,zma (A): -71.08801 -22.81600 x,y,z range (A): 65.34400 56.07700 48.27200 scale (grids/A): 2.451640 object centre (A): 11.96800 49.79650 -46.95200 number of atom coordinates read : 2976 total number of charged atoms : 2835 net assigned charge : -1.999988 assigned positive charge : 433.9566 centred at (gu) : 88.60796 89.66261 88.20664 assigned negative charge : -435.9572 centred at (gu) : 88.47238 90.14288 88.10307 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 146447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25628 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 68036 mr = 105079 m= 19859 mr = 54421 m= 3184 mr = 15407 m= 234 mr = 2193 m= 7 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 887 time to turn everything in is 1.370000 number of dielectric boundary points 60536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 22650 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) : 1.634427 object centre at (A) : 11.96800 49.79650 -46.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1109673 0.1386262 midg,1,midg; midg,igrid,midg -3.3872128E-02 6.6093214E-02 1,midg,midg; igrid,midg,midg -0.1766439 -0.4421761 gauss-seidel spectral radius is 0.9991380 estimated iterations to convergence 269 setup time was (sec) 1.690000 now iterating at: 06:56:53 rms-change max change #iterations 8.470925 311.2659 at 10iterations 4.731527 133.5663 at 20iterations 2.636954 61.91501 at 30iterations 1.461059 32.92561 at 40iterations 0.8103818 17.56542 at 50iterations 0.4474717 9.982651 at 60iterations 0.2468067 5.451494 at 70iterations 0.1359988 3.013929 at 80iterations 7.4973203E-02 1.545011 at 90iterations 4.1158684E-02 0.8200514 at 100iterations 2.2594145E-02 0.4661007 at 110iterations 1.2431842E-02 0.2744637 at 120iterations 6.8367431E-03 0.1423550 at 130iterations 3.7547986E-03 7.5744629E-02 at 140iterations 2.0575277E-03 4.4834137E-02 at 150iterations 1.1328250E-03 2.4241209E-02 at 160iterations 6.2276912E-04 1.3366699E-02 at 170iterations 3.4260517E-04 6.5269470E-03 at 180iterations finished qdiffx linear iterations at : 06:57:07 total time elapsed so far: 14.91000 # loops : 180 mean,max change (kT/e) : 3.4260517E-04 6.5269470E-03 energy calculations done at 14.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.08000 DelPhi exited at 06:57:07 15.083u 0.333s 0:15.72 98.0% 0+0k 0+0io 0pf+0w