Sun Oct 9 04:40:55 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 04:40:55 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 = 2693 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: 0.5894527 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): 29.69700 75.83200 ymin,ymax (A): 10.05000 70.44500 zmin,zma (A): -27.76200 24.54200 x,y,z range (A): 46.13500 60.39500 52.30400 scale (grids/A): 0.5894527 object centre (A): 52.76450 40.24750 -1.610000 number of atom coordinates read : 2693 total number of charged atoms : 2554 net assigned charge : 5.500029 assigned positive charge : 399.5162 centred at (gu) : 90.05780 91.49615 89.97784 assigned negative charge : -394.0174 centred at (gu) : 90.13233 91.50309 89.96383 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6170 nv = 96 ne = 84 npr = 53965 no. pairs analyzed = 53965 no. exposed pairs = 3676 no. arc points = 25537 no. surface atoms = 1228 nbur = 1465 mkacc time = 0.1300000 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 = 1.456000 m= 325 mr = 3059 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2505 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2969493E-09 2.0235280E-09 midg,1,midg; midg,igrid,midg 1.3236509E-09 2.0667936E-09 1,midg,midg; igrid,midg,midg 3.5735144E-09 -3.3603878E-10 gauss-seidel spectral radius is 0.9851213 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 04:40:56 rms-change max change #iterations 0.1002566 20.54522 at 10iterations 8.0141211E-03 1.458560 at 20iterations 6.8270625E-04 0.1011696 at 30iterations 9.8654695E-05 1.7598748E-02 at 40iterations 3.3441658E-05 5.5704117E-03 at 50iterations finished qdiffx linear iterations at : 04:40:59 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 3.3441658E-05 5.5704117E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 04:41:00 4.182u 0.253s 0:04.73 93.6% 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 Sun Oct 9 2011 at 04:41:00 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 = 2693 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: 1.768358 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): 29.69700 75.83200 ymin,ymax (A): 10.05000 70.44500 zmin,zma (A): -27.76200 24.54200 x,y,z range (A): 46.13500 60.39500 52.30400 scale (grids/A): 1.768358 object centre (A): 52.76450 40.24750 -1.610000 number of atom coordinates read : 2693 total number of charged atoms : 2554 net assigned charge : 5.500029 assigned positive charge : 399.5162 centred at (gu) : 90.17271 94.48775 89.93304 assigned negative charge : -394.0174 centred at (gu) : 90.39670 94.50916 89.89101 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25537 grid for indexing accessible points = 1.400000 m= 21402 mr = 44573 m= 2773 mr = 14333 m= 122 mr = 1371 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 31203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19847 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) : 0.5894527 object centre at (A) : 52.76450 40.24750 -1.610000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0990594E-03 1.0393447E-02 midg,1,midg; midg,igrid,midg -1.8585790E-02 1.9205213E-02 1,midg,midg; igrid,midg,midg 1.5736561E-02 2.8233996E-03 gauss-seidel spectral radius is 0.9984362 estimated iterations to convergence 201 setup time was (sec) 0.8500000 now iterating at: 04:41:01 rms-change max change #iterations 3.695345 159.3125 at 10iterations 1.631100 59.20326 at 20iterations 0.7217791 31.72509 at 30iterations 0.3218991 11.34796 at 40iterations 0.1423932 4.915558 at 50iterations 6.3211828E-02 2.194583 at 60iterations 2.7983494E-02 1.027145 at 70iterations 1.2470944E-02 0.4298778 at 80iterations 5.5573499E-03 0.1887741 at 90iterations 2.4625720E-03 8.3281517E-02 at 100iterations 1.1071479E-03 3.5575867E-02 at 110iterations 4.9913436E-04 1.7236233E-02 at 120iterations finished qdiffx linear iterations at : 04:41:10 total time elapsed so far: 9.720000 # loops : 120 mean,max change (kT/e) : 4.9913436E-04 1.7236233E-02 energy calculations done at 9.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.900000 DelPhi exited at 04:41:10 9.902u 0.323s 0:10.70 95.5% 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 04:41:11 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 = 2693 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: 2.652537 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): 29.69700 75.83200 ymin,ymax (A): 10.05000 70.44500 zmin,zma (A): -27.76200 24.54200 x,y,z range (A): 46.13500 60.39500 52.30400 scale (grids/A): 2.652537 object centre (A): 52.76450 40.24750 -1.610000 number of atom coordinates read : 2693 total number of charged atoms : 2554 net assigned charge : 5.500029 assigned positive charge : 399.5162 centred at (gu) : 90.25876 96.73149 89.89925 assigned negative charge : -394.0174 centred at (gu) : 90.59509 96.76363 89.83648 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 155887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25537 grid for indexing accessible points = 1.400000 m= 72173 mr = 109434 m= 22511 mr = 55965 m= 4518 mr = 16622 m= 497 mr = 2898 m= 22 mr = 248 m= 0 mr = 8 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 70433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 20416 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) : 1.768358 object centre at (A) : 52.76450 40.24750 -1.610000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8626186E-02 0.1451848 midg,1,midg; midg,igrid,midg -0.2489046 0.2878436 1,midg,midg; igrid,midg,midg 0.1703811 4.0711828E-02 gauss-seidel spectral radius is 0.9992110 estimated iterations to convergence 281 setup time was (sec) 1.700000 now iterating at: 04:41:12 rms-change max change #iterations 9.212684 331.5524 at 10iterations 5.367878 146.3953 at 20iterations 3.090237 83.60902 at 30iterations 1.773306 37.18428 at 40iterations 1.014537 26.38190 at 50iterations 0.5780384 15.30001 at 60iterations 0.3292073 8.686463 at 70iterations 0.1870361 3.862736 at 80iterations 0.1062481 2.255285 at 90iterations 6.0103990E-02 1.247490 at 100iterations 3.4037136E-02 0.7146282 at 110iterations 1.9256540E-02 0.3873959 at 120iterations 1.0893005E-02 0.2440763 at 130iterations 6.1817602E-03 0.1458092 at 140iterations 3.5135483E-03 8.3035469E-02 at 150iterations 2.0033969E-03 4.3266296E-02 at 160iterations 1.1574118E-03 2.4986267E-02 at 170iterations 6.8519742E-04 1.5861511E-02 at 180iterations finished qdiffx linear iterations at : 04:41:27 total time elapsed so far: 15.78000 # loops : 180 mean,max change (kT/e) : 6.8519742E-04 1.5861511E-02 energy calculations done at 15.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.96000 DelPhi exited at 04:41:27 15.963u 0.323s 0:16.55 98.3% 0+0k 0+0io 0pf+0w