Sat Oct 15 13:38:25 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 Sat Oct 15 2011 at 13:38:29 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5779034 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): 111.6270 173.2290 ymin,ymax (A): -41.43600 7.302000 zmin,zma (A): 50.29300 104.8670 x,y,z range (A): 61.60199 48.73800 54.57400 scale (grids/A): 0.5779034 object centre (A): 142.4280 -17.06700 77.58000 number of atom coordinates read : 2750 total number of charged atoms : 2607 net assigned charge : 16.00000 assigned positive charge : 403.7171 centred at (gu) : 90.24300 88.46404 88.83386 assigned negative charge : -387.7176 centred at (gu) : 90.16656 88.39950 88.66603 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6203 nv = 96 ne = 84 npr = 52051 no. pairs analyzed = 52051 no. exposed pairs = 4253 no. arc points = 31454 no. surface atoms = 1404 nbur = 1346 mkacc time = 0.1200000 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= 335 mr = 2581 m= 3 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3148 ## 394 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7870 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6195557E-10 4.7546598E-09 midg,1,midg; midg,igrid,midg 3.0096203E-09 3.1235003E-09 1,midg,midg; igrid,midg,midg 1.8208194E-09 4.9138471E-09 gauss-seidel spectral radius is 0.9845506 estimated iterations to convergence 66 setup time was (sec) 0.5200000 now iterating at: 13:38:33 rms-change max change #iterations 9.1027394E-02 17.73890 at 10iterations 6.7516416E-03 1.090675 at 20iterations 5.3373765E-04 8.7618351E-02 at 30iterations 4.8854054E-05 7.4987411E-03 at 40iterations 6.7737669E-06 7.6293945E-04 at 50iterations finished qdiffx linear iterations at : 13:38:41 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 6.7737669E-06 7.6293945E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 13:38:45 3.495u 0.204s 0:16.39 22.5% 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 Sat Oct 15 2011 at 13:38:50 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.733710 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): 111.6270 173.2290 ymin,ymax (A): -41.43600 7.302000 zmin,zma (A): 50.29300 104.8670 x,y,z range (A): 61.60199 48.73800 54.57400 scale (grids/A): 1.733710 object centre (A): 142.4280 -17.06700 77.58000 number of atom coordinates read : 2750 total number of charged atoms : 2607 net assigned charge : 16.00000 assigned positive charge : 403.7171 centred at (gu) : 90.72861 85.39207 86.50099 assigned negative charge : -387.7176 centred at (gu) : 90.49934 85.19831 85.99798 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 65802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31454 grid for indexing accessible points = 1.400000 m= 20540 mr = 38532 m= 2775 mr = 12928 m= 111 mr = 1269 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.4700000 number of dielectric boundary points 36491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 20234 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) : 0.5779034 object centre at (A) : 142.4280 -17.06700 77.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6150120E-04 2.5678528E-02 midg,1,midg; midg,igrid,midg 2.2023872E-02 1.3099917E-02 1,midg,midg; igrid,midg,midg 1.3258528E-02 3.3319529E-02 gauss-seidel spectral radius is 0.9984044 estimated iterations to convergence 199 setup time was (sec) 0.7700000 now iterating at: 13:38:54 rms-change max change #iterations 3.531811 171.7678 at 10iterations 1.552633 60.60343 at 20iterations 0.6783467 27.33664 at 30iterations 0.2977883 11.46140 at 40iterations 0.1305197 5.032428 at 50iterations 5.7013389E-02 1.895456 at 60iterations 2.5099559E-02 0.8591833 at 70iterations 1.1017510E-02 0.3746910 at 80iterations 4.8377248E-03 0.1789551 at 90iterations 2.1293650E-03 8.4817290E-02 at 100iterations 9.3413692E-04 3.8108826E-02 at 110iterations 4.1175063E-04 1.4116526E-02 at 120iterations finished qdiffx linear iterations at : 13:39:19 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 4.1175063E-04 1.4116526E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 13:39:23 9.408u 0.253s 0:34.17 28.2% 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 15 2011 at 13:39:25 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.600565 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): 111.6270 173.2290 ymin,ymax (A): -41.43600 7.302000 zmin,zma (A): 50.29300 104.8670 x,y,z range (A): 61.60199 48.73800 54.57400 scale (grids/A): 2.600565 object centre (A): 142.4280 -17.06700 77.58000 number of atom coordinates read : 2750 total number of charged atoms : 2607 net assigned charge : 16.00000 assigned positive charge : 403.7171 centred at (gu) : 91.09284 83.08796 84.75138 assigned negative charge : -387.7176 centred at (gu) : 90.74900 82.79749 83.99693 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 151749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31454 grid for indexing accessible points = 1.400000 m= 66831 mr = 95434 m= 22493 mr = 49259 m= 4573 mr = 16076 m= 417 mr = 2785 m= 12 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 1.120000 number of dielectric boundary points 82360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 20844 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) : 1.733710 object centre at (A) : 142.4280 -17.06700 77.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9759228E-02 0.3530792 midg,1,midg; midg,igrid,midg 0.2747807 0.1294807 1,midg,midg; igrid,midg,midg 0.1261605 0.2502291 gauss-seidel spectral radius is 0.9992242 estimated iterations to convergence 283 setup time was (sec) 1.420000 now iterating at: 13:39:32 rms-change max change #iterations 9.029266 274.4366 at 10iterations 5.316047 137.5191 at 20iterations 3.086123 90.84446 at 30iterations 1.781537 46.47767 at 40iterations 1.026361 28.90097 at 50iterations 0.5860296 14.46805 at 60iterations 0.3339641 8.586615 at 70iterations 0.1908353 4.658482 at 80iterations 0.1086667 2.409628 at 90iterations 6.1838914E-02 1.328876 at 100iterations 3.5127673E-02 0.7966365 at 110iterations 1.9941460E-02 0.4292669 at 120iterations 1.1332536E-02 0.2495451 at 130iterations 6.4308289E-03 0.1446991 at 140iterations 3.6349667E-03 8.4466934E-02 at 150iterations 2.0649070E-03 4.0664673E-02 at 160iterations 1.1689988E-03 2.5392532E-02 at 170iterations 6.6256389E-04 1.2836456E-02 at 180iterations finished qdiffx linear iterations at : 13:40:02 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 6.6256389E-04 1.2836456E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 13:40:06 11.334u 0.153s 0:40.92 28.0% 0+0k 0+0io 0pf+0w