Mon Oct 10 11:03:26 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 11:03:26 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5346 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5099921 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): -29.76300 40.04200 ymin,ymax (A): -28.15100 41.43400 zmin,zma (A): -34.17900 27.27200 x,y,z range (A): 69.80500 69.58501 61.45100 scale (grids/A): 0.5099921 object centre (A): 5.139500 6.641500 -3.453501 number of atom coordinates read : 5346 total number of charged atoms : 5190 net assigned charge : 10.00004 assigned positive charge : 848.7110 centred at (gu) : 89.90769 89.99901 89.97076 assigned negative charge : -838.7189 centred at (gu) : 89.89977 89.94873 89.99452 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8932 nv = 96 ne = 84 npr = 105232 no. pairs analyzed = 105232 no. exposed pairs = 6431 no. arc points = 44317 no. surface atoms = 2170 nbur = 3176 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 = 1.680000 m= 303 mr = 4887 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.5200000 number of dielectric boundary points 4338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4402 ## 676 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11884 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1019765E-10 6.6874575E-11 midg,1,midg; midg,igrid,midg -1.2227283E-11 2.8653202E-10 1,midg,midg; igrid,midg,midg 1.1736084E-10 1.5790770E-10 gauss-seidel spectral radius is 0.9803747 estimated iterations to convergence 59 setup time was (sec) 0.7500000 now iterating at: 11:03:27 rms-change max change #iterations 7.2313704E-02 10.22358 at 10iterations 4.2641796E-03 0.6607666 at 20iterations 5.9314992E-04 8.8479996E-02 at 30iterations 2.9398050E-04 4.2880297E-02 at 40iterations 1.5873130E-04 2.3389816E-02 at 50iterations finished qdiffx linear iterations at : 11:03:30 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 1.5873130E-04 2.3389816E-02 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 11:03:30 3.740u 0.216s 0:04.23 93.3% 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 Mon Oct 10 2011 at 11:03:30 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5346 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.529976 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): -29.76300 40.04200 ymin,ymax (A): -28.15100 41.43400 zmin,zma (A): -34.17900 27.27200 x,y,z range (A): 69.80500 69.58501 61.45100 scale (grids/A): 1.529976 object centre (A): 5.139500 6.641500 -3.453501 number of atom coordinates read : 5346 total number of charged atoms : 5190 net assigned charge : 10.00004 assigned positive charge : 848.7110 centred at (gu) : 89.72160 89.99556 89.91065 assigned negative charge : -838.7189 centred at (gu) : 89.69923 89.84608 89.98340 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 101560 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44317 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30077 mr = 71942 m= 2665 mr = 20700 m= 50 mr = 1166 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2090 time to turn everything in is 0.7400000 number of dielectric boundary points 40544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 622 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 38878 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) : 0.5099921 object centre at (A) : 5.139500 6.641500 -3.453501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0045593E-02 1.3301645E-03 midg,1,midg; midg,igrid,midg -1.7846230E-02 1.3815231E-02 1,midg,midg; igrid,midg,midg -9.5797041E-03 2.1694932E-02 gauss-seidel spectral radius is 0.9981574 estimated iterations to convergence 185 setup time was (sec) 1.050000 now iterating at: 11:03:31 rms-change max change #iterations 4.174183 176.2976 at 10iterations 1.729041 53.88903 at 20iterations 0.7190479 22.08529 at 30iterations 0.2993893 9.264299 at 40iterations 0.1242422 3.712570 at 50iterations 5.1757473E-02 1.514343 at 60iterations 2.1551965E-02 0.6773653 at 70iterations 9.0647275E-03 0.2780104 at 80iterations 3.8668697E-03 0.1307907 at 90iterations 1.7621666E-03 5.8719635E-02 at 100iterations 9.3385403E-04 3.2226563E-02 at 110iterations 6.0526893E-04 2.1269321E-02 at 120iterations finished qdiffx linear iterations at : 11:03:39 total time elapsed so far: 8.850000 # loops : 120 mean,max change (kT/e) : 6.0526893E-04 2.1269321E-02 energy calculations done at 8.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 11:03:40 9.047u 0.237s 0:09.55 97.0% 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 11:03:40 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5346 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: 2.294965 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): -29.76300 40.04200 ymin,ymax (A): -28.15100 41.43400 zmin,zma (A): -34.17900 27.27200 x,y,z range (A): 69.80500 69.58501 61.45100 scale (grids/A): 2.294965 object centre (A): 5.139500 6.641500 -3.453501 number of atom coordinates read : 5346 total number of charged atoms : 5190 net assigned charge : 10.00004 assigned positive charge : 848.7110 centred at (gu) : 89.58205 89.99284 89.86556 assigned negative charge : -838.7189 centred at (gu) : 89.54889 89.76915 89.97515 start vw surface at 0.2200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 236990 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44317 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 108470 mr = 176410 m= 27449 mr = 86365 m= 3745 mr = 20121 m= 145 mr = 2339 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 7120 time to turn everything in is 1.800000 number of dielectric boundary points 91540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 41412 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) : 1.529976 object centre at (A) : 5.139500 6.641500 -3.453501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1357611 -2.6357530E-02 midg,1,midg; midg,igrid,midg -0.3472822 0.2139180 1,midg,midg; igrid,midg,midg -0.2818100 0.6427633 gauss-seidel spectral radius is 0.9991831 estimated iterations to convergence 276 setup time was (sec) 2.160000 now iterating at: 11:03:42 rms-change max change #iterations 11.21588 345.8612 at 10iterations 6.489152 177.1224 at 20iterations 3.719256 91.02170 at 30iterations 2.118836 44.53207 at 40iterations 1.205705 27.43411 at 50iterations 0.6800166 12.03088 at 60iterations 0.3845429 8.203396 at 70iterations 0.2168094 4.192642 at 80iterations 0.1215591 2.492984 at 90iterations 6.8458073E-02 1.278726 at 100iterations 3.8488291E-02 0.7261610 at 110iterations 2.1602169E-02 0.3908539 at 120iterations 1.2137196E-02 0.2436154 at 130iterations 6.8385173E-03 0.1341968 at 140iterations 3.8784961E-03 7.8515530E-02 at 150iterations 2.2329397E-03 4.9154282E-02 at 160iterations 1.3318993E-03 2.8170586E-02 at 170iterations 8.4158214E-04 1.7769814E-02 at 180iterations finished qdiffx linear iterations at : 11:03:53 total time elapsed so far: 13.60000 # loops : 180 mean,max change (kT/e) : 8.4158214E-04 1.7769814E-02 energy calculations done at 13.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 11:03:54 13.799u 0.220s 0:14.30 97.9% 0+0k 0+0io 0pf+0w