Mon Oct 10 13:54:01 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+sph2.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 = amb2.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 13:54:01 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4092 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5870809 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): -25.32700 35.31200 ymin,ymax (A): 39.80600 96.06400 zmin,zma (A): 30.97900 90.57300 x,y,z range (A): 60.63900 56.25800 59.59399 scale (grids/A): 0.5870809 object centre (A): 4.992500 67.93500 60.77600 number of atom coordinates read : 4092 total number of charged atoms : 3936 net assigned charge : -1.485961 assigned positive charge : 609.9198 centred at (gu) : 90.64300 88.95837 88.82179 assigned negative charge : -611.4085 centred at (gu) : 90.50719 89.10607 88.99038 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 9149 nv = 96 ne = 84 npr = 86052 no. pairs analyzed = 86052 no. exposed pairs = 4515 no. arc points = 30880 no. surface atoms = 1552 nbur = 2540 mkacc time = 0.2400000 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 = 1.484000 m= 435 mr = 5379 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.5600000 number of dielectric boundary points 4152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3249 ## 358 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 11842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5632709E-09 -5.4233960E-09 midg,1,midg; midg,igrid,midg 6.3378027E-09 -4.9510871E-09 1,midg,midg; igrid,midg,midg -5.0299924E-09 5.2515605E-09 gauss-seidel spectral radius is 0.9851023 estimated iterations to convergence 67 setup time was (sec) 0.8700000 now iterating at: 13:54:02 rms-change max change #iterations 0.1261679 16.04040 at 10iterations 1.0916043E-02 1.442715 at 20iterations 1.4780626E-03 0.1988397 at 30iterations 4.3439056E-04 5.9405327E-02 at 40iterations 1.6022519E-04 2.2512436E-02 at 50iterations finished qdiffx linear iterations at : 13:54:06 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 1.6022519E-04 2.2512436E-02 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 13:54:06 4.332u 0.189s 0:04.88 92.4% 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 13:54:06 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4092 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.761243 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): -25.32700 35.31200 ymin,ymax (A): 39.80600 96.06400 zmin,zma (A): 30.97900 90.57300 x,y,z range (A): 60.63900 56.25800 59.59399 scale (grids/A): 1.761243 object centre (A): 4.992500 67.93500 60.77600 number of atom coordinates read : 4092 total number of charged atoms : 3936 net assigned charge : -1.485961 assigned positive charge : 609.9198 centred at (gu) : 91.92760 86.87367 86.46447 assigned negative charge : -611.4085 centred at (gu) : 91.52150 87.31773 86.97060 start vw surface at 0.2500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 101003 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30880 grid for indexing accessible points = 1.400000 m= 37506 mr = 73884 m= 5375 mr = 28433 m= 200 mr = 3334 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3691 time to turn everything in is 0.9300000 number of dielectric boundary points 38377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 280 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 30610 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) : 0.5870809 object centre at (A) : 4.992500 67.93500 60.77600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6979232E-02 -3.3458177E-02 midg,1,midg; midg,igrid,midg 2.9096927E-02 -1.8310778E-02 1,midg,midg; igrid,midg,midg -2.2628007E-02 3.8168903E-02 gauss-seidel spectral radius is 0.9985418 estimated iterations to convergence 208 setup time was (sec) 1.290000 now iterating at: 13:54:08 rms-change max change #iterations 4.684583 177.6555 at 10iterations 2.140433 62.65895 at 20iterations 0.9773207 28.50097 at 30iterations 0.4470478 12.12457 at 40iterations 0.2055828 5.820168 at 50iterations 9.4133429E-02 2.749226 at 60iterations 4.3268733E-02 1.273732 at 70iterations 1.9969435E-02 0.5799069 at 80iterations 9.2774304E-03 0.2716069 at 90iterations 4.4246172E-03 0.1357942 at 100iterations 2.1772729E-03 6.0624123E-02 at 110iterations 1.1493068E-03 3.2038450E-02 at 120iterations finished qdiffx linear iterations at : 13:54:16 total time elapsed so far: 9.850000 # loops : 120 mean,max change (kT/e) : 1.1493068E-03 3.2038450E-02 energy calculations done at 9.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.09000 DelPhi exited at 13:54:17 10.090u 0.252s 0:10.68 96.8% 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 Mon Oct 10 2011 at 13:54:17 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4092 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.641864 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): -25.32700 35.31200 ymin,ymax (A): 39.80600 96.06400 zmin,zma (A): 30.97900 90.57300 x,y,z range (A): 60.63900 56.25800 59.59399 scale (grids/A): 2.641864 object centre (A): 4.992500 67.93500 60.77600 number of atom coordinates read : 4092 total number of charged atoms : 3936 net assigned charge : -1.485961 assigned positive charge : 609.9198 centred at (gu) : 92.89124 85.31035 84.69629 assigned negative charge : -611.4085 centred at (gu) : 92.28201 85.97652 85.45570 start vw surface at 0.2500000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 234092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30880 grid for indexing accessible points = 1.400000 m= 122672 mr = 178314 m= 43801 mr = 102601 m= 9410 mr = 35681 m= 981 mr = 7119 m= 29 mr = 592 m= 0 mr = 6 time to grow re-entrant surface = 1.410000 no. cavity mid-points inaccessible to solvent = 13057 time to turn everything in is 2.330000 number of dielectric boundary points 86672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 31472 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) : 1.761243 object centre at (A) : 4.992500 67.93500 60.77600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9238057 -0.3731195 midg,1,midg; midg,igrid,midg 0.3700495 -0.2648669 1,midg,midg; igrid,midg,midg -0.3591396 0.3850083 gauss-seidel spectral radius is 0.9992564 estimated iterations to convergence 289 setup time was (sec) 2.730000 now iterating at: 13:54:20 rms-change max change #iterations 11.42801 562.9464 at 10iterations 6.694831 144.4746 at 20iterations 3.895283 69.92381 at 30iterations 2.268925 49.90488 at 40iterations 1.313942 23.25999 at 50iterations 0.7605407 11.95357 at 60iterations 0.4386027 7.749670 at 70iterations 0.2530952 4.378620 at 80iterations 0.1461644 2.419348 at 90iterations 8.4105775E-02 1.341702 at 100iterations 4.8607439E-02 0.7694819 at 110iterations 2.8049050E-02 0.4764595 at 120iterations 1.6291544E-02 0.2566738 at 130iterations 9.4944825E-03 0.1531982 at 140iterations 5.6194775E-03 8.8268280E-02 at 150iterations 3.4008329E-03 5.5245399E-02 at 160iterations 2.1309084E-03 3.6068916E-02 at 170iterations 1.4047184E-03 2.4574757E-02 at 180iterations finished qdiffx linear iterations at : 13:54:32 total time elapsed so far: 15.16000 # loops : 180 mean,max change (kT/e) : 1.4047184E-03 2.4574757E-02 energy calculations done at 15.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.41000 DelPhi exited at 13:54:33 15.411u 0.230s 0:16.05 97.4% 0+0k 0+0io 0pf+0w