Sun Oct 9 19:33:12 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 Sun Oct 9 2011 at 19:33:13 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 = 3011 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: 0.5434285 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): -3.089000 62.42100 ymin,ymax (A): -13.16200 35.03700 zmin,zma (A): 18.70300 70.80100 x,y,z range (A): 65.51000 48.19900 52.09800 scale (grids/A): 0.5434285 object centre (A): 29.66600 10.93750 44.75200 number of atom coordinates read : 3011 total number of charged atoms : 2869 net assigned charge : 11.50002 assigned positive charge : 456.7693 centred at (gu) : 90.63762 89.64159 89.80454 assigned negative charge : -445.2704 centred at (gu) : 90.76605 89.66602 89.76102 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5802 nv = 96 ne = 84 npr = 59494 no. pairs analyzed = 59494 no. exposed pairs = 3798 no. arc points = 26909 no. surface atoms = 1279 nbur = 1732 mkacc time = 0.2000000 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= 236 mr = 2999 m= 0 mr = 8 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2749 ## 367 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 7609 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0743031E-10 8.7290986E-10 midg,1,midg; midg,igrid,midg 8.7430663E-10 4.6446247E-10 1,midg,midg; igrid,midg,midg 1.2118383E-09 -1.6528463E-10 gauss-seidel spectral radius is 0.9825468 estimated iterations to convergence 62 setup time was (sec) 0.7800000 now iterating at: 19:33:14 rms-change max change #iterations 6.8474360E-02 13.23910 at 10iterations 4.8440411E-03 0.7797394 at 20iterations 6.3044991E-04 9.7654343E-02 at 30iterations 2.0849568E-04 3.2052755E-02 at 40iterations 8.1077254E-05 1.2795210E-02 at 50iterations finished qdiffx linear iterations at : 19:33:18 total time elapsed so far: 4.850000 # loops : 50 mean,max change (kT/e) : 8.1077254E-05 1.2795210E-02 energy calculations done at 4.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.070000 DelPhi exited at 19:33:18 5.072u 0.440s 0:05.79 95.1% 0+0k 0+0io 6pf+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 Sun Oct 9 2011 at 19:33:18 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 = 3011 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: 1.630285 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): -3.089000 62.42100 ymin,ymax (A): -13.16200 35.03700 zmin,zma (A): 18.70300 70.80100 x,y,z range (A): 65.51000 48.19900 52.09800 scale (grids/A): 1.630285 object centre (A): 29.66600 10.93750 44.75200 number of atom coordinates read : 3011 total number of charged atoms : 2869 net assigned charge : 11.50002 assigned positive charge : 456.7693 centred at (gu) : 91.91192 88.92393 89.41300 assigned negative charge : -445.2704 centred at (gu) : 92.29781 88.99783 89.28282 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 65110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26909 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20759 mr = 44479 m= 2261 mr = 14228 m= 76 mr = 1158 m= 0 mr = 1 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 372 time to turn everything in is 0.6700000 number of dielectric boundary points 28340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 321 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 21968 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) : 0.5434285 object centre at (A) : 29.66600 10.93750 44.75200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1315077E-03 7.1771746E-03 midg,1,midg; midg,igrid,midg 1.0694595E-02 5.4262062E-03 1,midg,midg; igrid,midg,midg 2.2273535E-02 9.2539666E-03 gauss-seidel spectral radius is 0.9981821 estimated iterations to convergence 186 setup time was (sec) 1.010000 now iterating at: 19:33:20 rms-change max change #iterations 3.315093 157.7223 at 10iterations 1.380763 61.79844 at 20iterations 0.5769421 21.56306 at 30iterations 0.2400887 12.06652 at 40iterations 0.1003931 3.434331 at 50iterations 4.1831248E-02 1.676264 at 60iterations 1.7491918E-02 0.7657766 at 70iterations 7.3415278E-03 0.2606506 at 80iterations 3.0945723E-03 0.1067607 at 90iterations 1.3354357E-03 4.9161911E-02 at 100iterations 6.1240303E-04 2.3900986E-02 at 110iterations 3.1500912E-04 1.1981010E-02 at 120iterations finished qdiffx linear iterations at : 19:33:30 total time elapsed so far: 11.24000 # loops : 120 mean,max change (kT/e) : 3.1500912E-04 1.1981010E-02 energy calculations done at 11.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.47000 DelPhi exited at 19:33:31 11.474u 0.506s 0:12.29 97.3% 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 Sun Oct 9 2011 at 19:33:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3011 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: 2.445428 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): -3.089000 62.42100 ymin,ymax (A): -13.16200 35.03700 zmin,zma (A): 18.70300 70.80100 x,y,z range (A): 65.51000 48.19900 52.09800 scale (grids/A): 2.445428 object centre (A): 29.66600 10.93750 44.75200 number of atom coordinates read : 3011 total number of charged atoms : 2869 net assigned charge : 11.50002 assigned positive charge : 456.7693 centred at (gu) : 92.86785 88.38580 89.11925 assigned negative charge : -445.2704 centred at (gu) : 93.44676 88.49661 88.92421 start vw surface at 0.1800000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 150828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26909 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 71510 mr = 108663 m= 21318 mr = 56451 m= 3627 mr = 15914 m= 300 mr = 2369 m= 4 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1310 time to turn everything in is 1.880000 number of dielectric boundary points 64036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 22929 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) : 1.630285 object centre at (A) : 29.66600 10.93750 44.75200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3956259E-02 0.1009336 midg,1,midg; midg,igrid,midg 0.1656625 6.5516651E-02 1,midg,midg; igrid,midg,midg 0.3878714 0.2620910 gauss-seidel spectral radius is 0.9991371 estimated iterations to convergence 269 setup time was (sec) 2.250000 now iterating at: 19:33:33 rms-change max change #iterations 8.627837 266.3553 at 10iterations 4.876525 140.6781 at 20iterations 2.739293 68.05933 at 30iterations 1.530424 38.75526 at 40iterations 0.8530695 20.30103 at 50iterations 0.4730318 11.03292 at 60iterations 0.2622854 7.291146 at 70iterations 0.1452152 3.157377 at 80iterations 8.0115549E-02 1.928909 at 90iterations 4.4194516E-02 1.088238 at 100iterations 2.4412623E-02 0.5525665 at 110iterations 1.3484054E-02 0.2845116 at 120iterations 7.4361074E-03 0.1671338 at 130iterations 4.0985146E-03 8.9760780E-02 at 140iterations 2.2647881E-03 5.0119400E-02 at 150iterations 1.2530831E-03 2.5829315E-02 at 160iterations 6.9887046E-04 1.7999649E-02 at 170iterations 3.9583485E-04 8.6345673E-03 at 180iterations finished qdiffx linear iterations at : 19:33:50 total time elapsed so far: 19.14000 # loops : 180 mean,max change (kT/e) : 3.9583485E-04 8.6345673E-03 energy calculations done at 19.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.34000 DelPhi exited at 19:33:51 19.343u 0.527s 0:20.14 98.6% 0+0k 0+0io 0pf+0w