Tue Oct 11 04:17:38 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 04:17:38 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6613536 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): -14.88100 33.00600 ymin,ymax (A): 7.513999 55.95500 zmin,zma (A): 25.63000 79.45900 x,y,z range (A): 47.88700 48.44100 53.82900 scale (grids/A): 0.6613536 object centre (A): 9.062500 31.73450 52.54450 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 4.140018 assigned positive charge : 414.1557 centred at (gu) : 90.12432 90.51054 88.60263 assigned negative charge : -410.0164 centred at (gu) : 90.41136 90.31416 88.62756 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8018 nv = 96 ne = 84 npr = 56589 no. pairs analyzed = 56589 no. exposed pairs = 3329 no. arc points = 23022 no. surface atoms = 1121 nbur = 1629 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 4608 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3100000 number of dielectric boundary points 3819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2251 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9517 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1557739E-08 4.1584798E-09 midg,1,midg; midg,igrid,midg -2.9123596E-08 5.8269535E-08 1,midg,midg; igrid,midg,midg 6.9123672E-08 -5.4566808E-08 gauss-seidel spectral radius is 0.9881595 estimated iterations to convergence 75 setup time was (sec) 0.5200000 now iterating at: 04:17:38 rms-change max change #iterations 0.1732787 22.33324 at 10iterations 1.8861622E-02 2.670815 at 20iterations 2.1136829E-03 0.3288221 at 30iterations 2.8212319E-04 3.9997101E-02 at 40iterations 5.6935642E-05 8.3198547E-03 at 50iterations finished qdiffx linear iterations at : 04:17:41 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 5.6935642E-05 8.3198547E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 04:17:41 3.089u 0.139s 0:03.74 85.8% 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 04:17:41 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.984061 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): -14.88100 33.00600 ymin,ymax (A): 7.513999 55.95500 zmin,zma (A): 25.63000 79.45900 x,y,z range (A): 47.88700 48.44100 53.82900 scale (grids/A): 1.984061 object centre (A): 9.062500 31.73450 52.54450 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 4.140018 assigned positive charge : 414.1557 centred at (gu) : 90.37244 91.53131 85.80737 assigned negative charge : -410.0164 centred at (gu) : 91.23376 90.94227 85.88245 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23022 grid for indexing accessible points = 1.400000 m= 32006 mr = 61835 m= 5111 mr = 23864 m= 300 mr = 3137 m= 3 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 436 time to turn everything in is 0.6000000 number of dielectric boundary points 35316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20520 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) : 0.6613536 object centre at (A) : 9.062500 31.73450 52.54450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6405931E-03 -1.4956041E-02 midg,1,midg; midg,igrid,midg -1.5112558E-02 4.3041516E-02 1,midg,midg; igrid,midg,midg 8.0227636E-02 -1.8583326E-02 gauss-seidel spectral radius is 0.9987497 estimated iterations to convergence 224 setup time was (sec) 0.8500000 now iterating at: 04:17:42 rms-change max change #iterations 4.777884 211.0286 at 10iterations 2.325777 84.00981 at 20iterations 1.124678 33.94146 at 30iterations 0.5456353 15.18482 at 40iterations 0.2651281 8.324167 at 50iterations 0.1282268 3.726856 at 60iterations 6.2185504E-02 2.037720 at 70iterations 3.0168070E-02 0.9256535 at 80iterations 1.4688595E-02 0.3899755 at 90iterations 7.1143699E-03 0.2020798 at 100iterations 3.4662387E-03 0.1089439 at 110iterations 1.6895962E-03 5.3394318E-02 at 120iterations finished qdiffx linear iterations at : 04:17:49 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.6895962E-03 5.3394318E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 04:17:50 7.471u 0.194s 0:08.21 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 04:17:50 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.976091 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): -14.88100 33.00600 ymin,ymax (A): 7.513999 55.95500 zmin,zma (A): 25.63000 79.45900 x,y,z range (A): 47.88700 48.44100 53.82900 scale (grids/A): 2.976091 object centre (A): 9.062500 31.73450 52.54450 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 4.140018 assigned positive charge : 414.1557 centred at (gu) : 90.55838 92.29681 83.71088 assigned negative charge : -410.0164 centred at (gu) : 91.85059 91.41329 83.82367 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 200445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23022 grid for indexing accessible points = 1.400000 m= 103840 mr = 148854 m= 37466 mr = 85900 m= 8995 mr = 30191 m= 1375 mr = 6680 m= 109 mr = 910 m= 6 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 1491 time to turn everything in is 1.500000 number of dielectric boundary points 79660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 20780 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) : 1.984061 object centre at (A) : 9.062500 31.73450 52.54450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2224453 -0.1367934 midg,1,midg; midg,igrid,midg -0.1613067 0.4786559 1,midg,midg; igrid,midg,midg 0.6807967 -0.1054575 gauss-seidel spectral radius is 0.9992870 estimated iterations to convergence 295 setup time was (sec) 1.780000 now iterating at: 04:17:52 rms-change max change #iterations 10.90798 320.4348 at 10iterations 6.426015 142.1909 at 20iterations 3.771032 77.07350 at 30iterations 2.214784 54.44045 at 40iterations 1.295585 24.80779 at 50iterations 0.7588402 13.53652 at 60iterations 0.4425053 7.231427 at 70iterations 0.2586751 4.310894 at 80iterations 0.1507955 2.592402 at 90iterations 8.8016719E-02 1.455799 at 100iterations 5.1294897E-02 0.8533096 at 110iterations 2.9985914E-02 0.5259900 at 120iterations 1.7435145E-02 0.2923527 at 130iterations 1.0200924E-02 0.1760234 at 140iterations 5.9888912E-03 0.1071606 at 150iterations 3.5455774E-03 5.9593201E-02 at 160iterations 2.1230516E-03 3.9897919E-02 at 170iterations 1.2969752E-03 2.5966644E-02 at 180iterations finished qdiffx linear iterations at : 04:18:02 total time elapsed so far: 11.83000 # loops : 180 mean,max change (kT/e) : 1.2969752E-03 2.5966644E-02 energy calculations done at 11.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 04:18:02 12.009u 0.197s 0:12.48 97.6% 0+0k 0+0io 0pf+0w