Sat Oct 8 11:39:42 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 Sat Oct 8 2011 at 11:39:42 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4473 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5497984 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): -27.75400 35.35700 ymin,ymax (A): 34.63100 99.38200 zmin,zma (A): 30.77000 88.93700 x,y,z range (A): 63.11100 64.75101 58.16701 scale (grids/A): 0.5497984 object centre (A): 3.801499 67.00650 59.85350 number of atom coordinates read : 4473 total number of charged atoms : 4313 net assigned charge : -5.485951 assigned positive charge : 674.4012 centred at (gu) : 90.95810 88.28111 89.17387 assigned negative charge : -679.8902 centred at (gu) : 90.82413 88.37363 89.33059 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8515 nv = 96 ne = 84 npr = 94298 no. pairs analyzed = 94298 no. exposed pairs = 4959 no. arc points = 33783 no. surface atoms = 1692 nbur = 2781 mkacc time = 0.1600000 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= 300 mr = 4896 m= 0 mr = 20 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.3100000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3505 ## 444 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 11445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6619890E-09 -1.8830486E-09 midg,1,midg; midg,igrid,midg 9.7133379E-10 -1.0093915E-09 1,midg,midg; igrid,midg,midg -1.6062366E-09 1.3936219E-09 gauss-seidel spectral radius is 0.9830433 estimated iterations to convergence 63 setup time was (sec) 0.5100000 now iterating at: 11:39:43 rms-change max change #iterations 9.6196584E-02 13.22255 at 10iterations 6.9329883E-03 1.224148 at 20iterations 6.8075565E-04 9.9647522E-02 at 30iterations 1.5888183E-04 2.3524165E-02 at 40iterations 5.3326865E-05 8.3161592E-03 at 50iterations finished qdiffx linear iterations at : 11:39:46 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 5.3326865E-05 8.3161592E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 11:39:47 3.701u 0.196s 0:04.49 86.6% 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 Sat Oct 8 2011 at 11:39:47 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4473 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.649395 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): -27.75400 35.35700 ymin,ymax (A): 34.63100 99.38200 zmin,zma (A): 30.77000 88.93700 x,y,z range (A): 63.11100 64.75101 58.16701 scale (grids/A): 1.649395 object centre (A): 3.801499 67.00650 59.85350 number of atom coordinates read : 4473 total number of charged atoms : 4313 net assigned charge : -5.485951 assigned positive charge : 674.4012 centred at (gu) : 92.87291 84.84209 87.52003 assigned negative charge : -679.8902 centred at (gu) : 92.47202 85.12051 87.99107 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 96908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30971 mr = 70467 m= 3361 mr = 22663 m= 86 mr = 1882 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 6364 time to turn everything in is 0.4700000 number of dielectric boundary points 36305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33085 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) : 0.5497984 object centre at (A) : 3.801499 67.00650 59.85350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0689746E-02 -2.1175493E-02 midg,1,midg; midg,igrid,midg 1.8824110E-02 -3.5321189E-03 1,midg,midg; igrid,midg,midg -2.5656387E-02 2.5989143E-02 gauss-seidel spectral radius is 0.9983519 estimated iterations to convergence 196 setup time was (sec) 0.7100000 now iterating at: 11:39:48 rms-change max change #iterations 4.311965 178.5982 at 10iterations 1.877067 55.15900 at 20iterations 0.8203165 24.78445 at 30iterations 0.3578337 10.06230 at 40iterations 0.1561079 4.461371 at 50iterations 6.7818314E-02 2.204632 at 60iterations 2.9587587E-02 0.8629341 at 70iterations 1.2908332E-02 0.3988552 at 80iterations 5.6360057E-03 0.1789398 at 90iterations 2.4869754E-03 7.2792053E-02 at 100iterations 1.1084981E-03 3.2619715E-02 at 110iterations 5.0724234E-04 1.5362263E-02 at 120iterations finished qdiffx linear iterations at : 11:39:55 total time elapsed so far: 8.230000 # loops : 120 mean,max change (kT/e) : 5.0724234E-04 1.5362263E-02 energy calculations done at 8.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 11:39:56 8.370u 0.236s 0:09.01 95.4% 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 Sat Oct 8 2011 at 11:39:56 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4473 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.474093 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): -27.75400 35.35700 ymin,ymax (A): 34.63100 99.38200 zmin,zma (A): 30.77000 88.93700 x,y,z range (A): 63.11100 64.75101 58.16701 scale (grids/A): 2.474093 object centre (A): 3.801499 67.00650 59.85350 number of atom coordinates read : 4473 total number of charged atoms : 4313 net assigned charge : -5.485951 assigned positive charge : 674.4012 centred at (gu) : 94.30913 82.26261 86.27970 assigned negative charge : -679.8902 centred at (gu) : 93.70784 82.68065 86.98652 start vw surface at 0.1100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 225748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 108176 mr = 171369 m= 31125 mr = 88776 m= 5448 mr = 24544 m= 399 mr = 3946 m= 7 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 21724 time to turn everything in is 1.160000 number of dielectric boundary points 82050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 34461 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) : 1.649395 object centre at (A) : 3.801499 67.00650 59.85350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3832871 -0.2679515 midg,1,midg; midg,igrid,midg 0.3417981 9.2791557E-02 1,midg,midg; igrid,midg,midg -0.3628071 0.3252043 gauss-seidel spectral radius is 0.9992055 estimated iterations to convergence 280 setup time was (sec) 1.410000 now iterating at: 11:39:57 rms-change max change #iterations 10.91896 295.6117 at 10iterations 6.237315 120.9208 at 20iterations 3.568659 74.47698 at 30iterations 2.030637 43.83466 at 40iterations 1.153719 21.68748 at 50iterations 0.6541345 11.22328 at 60iterations 0.3697341 6.790760 at 70iterations 0.2093968 3.567894 at 80iterations 0.1180565 2.053631 at 90iterations 6.6793501E-02 1.162312 at 100iterations 3.7669279E-02 0.7004592 at 110iterations 2.1306343E-02 0.3449850 at 120iterations 1.2024268E-02 0.1999111 at 130iterations 6.8014711E-03 0.1146166 at 140iterations 3.8544144E-03 6.5130711E-02 at 150iterations 2.1956279E-03 3.6869049E-02 at 160iterations 1.2623594E-03 2.1070480E-02 at 170iterations 7.3803746E-04 1.4227629E-02 at 180iterations finished qdiffx linear iterations at : 11:40:10 total time elapsed so far: 13.66000 # loops : 180 mean,max change (kT/e) : 7.3803746E-04 1.4227629E-02 energy calculations done at 13.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.79000 DelPhi exited at 11:40:10 13.795u 0.252s 0:14.38 97.6% 0+0k 0+0io 0pf+0w