Mon Oct 10 00:16:31 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 00:16:31 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3206 !!! WARNING: HIY 180 has a net charge of 0.2000 !!! WARNING: ZN3 380 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5551917 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): -3.653000 60.46900 ymin,ymax (A): -25.42900 28.35900 zmin,zma (A): -22.32500 24.83300 x,y,z range (A): 64.12199 53.78800 47.15800 scale (grids/A): 0.5551917 object centre (A): 28.40800 1.464999 1.254000 number of atom coordinates read : 3206 total number of charged atoms : 3067 net assigned charge : -1.899981 assigned positive charge : 472.6870 centred at (gu) : 90.37588 88.97734 89.07337 assigned negative charge : -474.5883 centred at (gu) : 90.48894 88.95360 88.96196 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6357 nv = 96 ne = 84 npr = 66440 no. pairs analyzed = 66440 no. exposed pairs = 3737 no. arc points = 26312 no. surface atoms = 1272 nbur = 1934 mkacc time = 0.1100000 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 = 1.540000 m= 263 mr = 3528 m= 3 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2300000 number of dielectric boundary points 3083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2627 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8343 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5983438E-09 7.4931161E-10 midg,1,midg; midg,igrid,midg -4.9381499E-10 6.6114100E-11 1,midg,midg; igrid,midg,midg 8.7348745E-10 -1.4122433E-09 gauss-seidel spectral radius is 0.9832810 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 00:16:31 rms-change max change #iterations 8.3638325E-02 12.59317 at 10iterations 5.9954985E-03 0.9204025 at 20iterations 6.3463446E-04 0.1224976 at 30iterations 1.7265383E-04 4.0473938E-02 at 40iterations 6.1066909E-05 1.4165878E-02 at 50iterations finished qdiffx linear iterations at : 00:16:34 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 6.1066909E-05 1.4165878E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 00:16:35 3.482u 0.171s 0:04.20 86.9% 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 Mon Oct 10 2011 at 00:16:35 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3206 !!! WARNING: HIY 180 has a net charge of 0.2000 !!! WARNING: ZN3 380 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.665575 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): -3.653000 60.46900 ymin,ymax (A): -25.42900 28.35900 zmin,zma (A): -22.32500 24.83300 x,y,z range (A): 64.12199 53.78800 47.15800 scale (grids/A): 1.665575 object centre (A): 28.40800 1.464999 1.254000 number of atom coordinates read : 3206 total number of charged atoms : 3067 net assigned charge : -1.899981 assigned positive charge : 472.6870 centred at (gu) : 91.12688 86.93144 87.21909 assigned negative charge : -474.5883 centred at (gu) : 91.46660 86.86078 86.88560 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26312 grid for indexing accessible points = 1.400000 m= 23180 mr = 50183 m= 2704 mr = 16648 m= 76 mr = 1425 m= 0 mr = 10 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1271 time to turn everything in is 0.3400000 number of dielectric boundary points 28703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 23626 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) : 0.5551917 object centre at (A) : 28.40800 1.464999 1.254000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5324435E-03 1.0486471E-02 midg,1,midg; midg,igrid,midg -1.1274050E-02 -6.0215420E-03 1,midg,midg; igrid,midg,midg 1.1935987E-02 -2.0509103E-02 gauss-seidel spectral radius is 0.9982775 estimated iterations to convergence 191 setup time was (sec) 0.5600000 now iterating at: 00:16:36 rms-change max change #iterations 3.572151 152.0977 at 10iterations 1.519445 52.20943 at 20iterations 0.6511344 24.55383 at 30iterations 0.2777416 9.925709 at 40iterations 0.1182254 3.943066 at 50iterations 5.0760210E-02 1.583861 at 60iterations 2.1677686E-02 0.8124549 at 70iterations 9.3540587E-03 0.3025255 at 80iterations 4.0756278E-03 0.1441078 at 90iterations 1.8384792E-03 6.2246323E-02 at 100iterations 8.9399301E-04 3.5305023E-02 at 110iterations 4.8873207E-04 2.1240234E-02 at 120iterations finished qdiffx linear iterations at : 00:16:43 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 4.8873207E-04 2.1240234E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 00:16:43 7.817u 0.206s 0:08.29 96.6% 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 00:16:43 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3206 !!! WARNING: HIY 180 has a net charge of 0.2000 !!! WARNING: ZN3 380 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.498363 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): -3.653000 60.46900 ymin,ymax (A): -25.42900 28.35900 zmin,zma (A): -22.32500 24.83300 x,y,z range (A): 64.12199 53.78800 47.15800 scale (grids/A): 2.498363 object centre (A): 28.40800 1.464999 1.254000 number of atom coordinates read : 3206 total number of charged atoms : 3067 net assigned charge : -1.899981 assigned positive charge : 472.6870 centred at (gu) : 91.69011 85.39690 85.82832 assigned negative charge : -474.5883 centred at (gu) : 92.19995 85.29095 85.32834 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 164977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26312 grid for indexing accessible points = 1.400000 m= 79091 mr = 122122 m= 24353 mr = 64211 m= 4207 mr = 18990 m= 320 mr = 2865 m= 10 mr = 140 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 4462 time to turn everything in is 0.8400000 number of dielectric boundary points 64630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 24511 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) : 1.665575 object centre at (A) : 28.40800 1.464999 1.254000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7784453E-02 0.1631723 midg,1,midg; midg,igrid,midg -0.1193701 -7.4644953E-02 1,midg,midg; igrid,midg,midg 0.2266648 -0.3251608 gauss-seidel spectral radius is 0.9991607 estimated iterations to convergence 273 setup time was (sec) 1.080000 now iterating at: 00:16:45 rms-change max change #iterations 9.030289 293.6874 at 10iterations 5.108212 123.1054 at 20iterations 2.864044 71.37186 at 30iterations 1.607706 40.20817 at 40iterations 0.8976029 20.71153 at 50iterations 0.5021136 11.19333 at 60iterations 0.2788613 6.569645 at 70iterations 0.1554087 3.034960 at 80iterations 8.6443365E-02 1.881245 at 90iterations 4.8091456E-02 0.9971237 at 100iterations 2.6784550E-02 0.5780268 at 110iterations 1.4894084E-02 0.3004570 at 120iterations 8.3169667E-03 0.1610966 at 130iterations 4.6759648E-03 0.1031197 at 140iterations 2.6628675E-03 5.5442810E-02 at 150iterations 1.5539782E-03 3.5505295E-02 at 160iterations 9.4803498E-04 2.2876740E-02 at 170iterations 6.1540928E-04 1.5245438E-02 at 180iterations finished qdiffx linear iterations at : 00:16:56 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 6.1540928E-04 1.5245438E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 00:16:56 12.332u 0.215s 0:12.82 97.8% 0+0k 0+0io 0pf+0w