Sat Oct 8 20:25:21 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 8 2011 at 20:25:21 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 = 2587 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6300885 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): -10.43000 38.59600 ymin,ymax (A): -22.17000 24.67500 zmin,zma (A): -12.48800 44.01200 x,y,z range (A): 49.02600 46.84500 56.50000 scale (grids/A): 0.6300885 object centre (A): 14.08300 1.252500 15.76200 number of atom coordinates read : 2587 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 88.56757 89.28187 89.94370 assigned negative charge : -387.9955 centred at (gu) : 88.45695 89.31541 89.83679 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6759 nv = 96 ne = 84 npr = 54010 no. pairs analyzed = 54010 no. exposed pairs = 3040 no. arc points = 21933 no. surface atoms = 1017 nbur = 1570 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3737 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.3300000 number of dielectric boundary points 3292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2195 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8270 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1273381E-09 1.3672810E-08 midg,1,midg; midg,igrid,midg 8.7031609E-09 1.3342745E-09 1,midg,midg; igrid,midg,midg -7.5381079E-09 1.0397118E-08 gauss-seidel spectral radius is 0.9869481 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 20:25:21 rms-change max change #iterations 0.1343277 19.09039 at 10iterations 1.2974959E-02 2.321042 at 20iterations 1.2550158E-03 0.1883307 at 30iterations 1.1957711E-04 1.9176483E-02 at 40iterations 1.1679983E-05 1.5773773E-03 at 50iterations finished qdiffx linear iterations at : 20:25:24 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.1679983E-05 1.5773773E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 20:25:24 3.122u 0.152s 0:03.55 92.1% 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 20:25:24 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 = 2587 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: 1.890265 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): -10.43000 38.59600 ymin,ymax (A): -22.17000 24.67500 zmin,zma (A): -12.48800 44.01200 x,y,z range (A): 49.02600 46.84500 56.50000 scale (grids/A): 1.890265 object centre (A): 14.08300 1.252500 15.76200 number of atom coordinates read : 2587 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 85.70201 87.84501 89.83047 assigned negative charge : -387.9955 centred at (gu) : 85.37068 87.94594 89.51018 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21933 grid for indexing accessible points = 1.400000 m= 25454 mr = 50857 m= 3789 mr = 18813 m= 209 mr = 2301 m= 5 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 4026 time to turn everything in is 0.5000000 number of dielectric boundary points 30276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19349 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) : 0.6300885 object centre at (A) : 14.08300 1.252500 15.76200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9420383E-02 2.4769336E-02 midg,1,midg; midg,igrid,midg 1.3861004E-02 4.9206032E-03 1,midg,midg; igrid,midg,midg -4.0401239E-03 3.5627134E-02 gauss-seidel spectral radius is 0.9986102 estimated iterations to convergence 213 setup time was (sec) 0.7600000 now iterating at: 20:25:25 rms-change max change #iterations 4.114439 174.9214 at 10iterations 1.914602 61.94936 at 20iterations 0.8879058 32.88135 at 30iterations 0.4134526 12.92350 at 40iterations 0.1929505 5.961658 at 50iterations 8.9947671E-02 3.096449 at 60iterations 4.1618805E-02 1.311909 at 70iterations 1.9422207E-02 0.6243396 at 80iterations 9.0429382E-03 0.2845411 at 90iterations 4.2096134E-03 0.1320839 at 100iterations 1.9630890E-03 6.1251640E-02 at 110iterations 9.1089908E-04 2.9209614E-02 at 120iterations finished qdiffx linear iterations at : 20:25:31 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 9.1089908E-04 2.9209614E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 20:25:32 6.887u 0.170s 0:07.33 96.1% 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 20:25:32 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 = 2587 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: 2.835398 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): -10.43000 38.59600 ymin,ymax (A): -22.17000 24.67500 zmin,zma (A): -12.48800 44.01200 x,y,z range (A): 49.02600 46.84500 56.50000 scale (grids/A): 2.835398 object centre (A): 14.08300 1.252500 15.76200 number of atom coordinates read : 2587 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 83.55282 86.76743 89.74561 assigned negative charge : -387.9955 centred at (gu) : 83.05593 86.91880 89.26508 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 168663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21933 grid for indexing accessible points = 1.400000 m= 83902 mr = 122994 m= 28736 mr = 69162 m= 6714 mr = 22901 m= 851 mr = 5007 m= 48 mr = 538 m= 0 mr = 17 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 13282 time to turn everything in is 1.230000 number of dielectric boundary points 68295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19718 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) : 1.890265 object centre at (A) : 14.08300 1.252500 15.76200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1352419 0.2739639 midg,1,midg; midg,igrid,midg 0.1591626 5.7457559E-02 1,midg,midg; igrid,midg,midg -1.6930765E-02 0.4408842 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 1.510000 now iterating at: 20:25:33 rms-change max change #iterations 9.708632 395.1942 at 10iterations 5.622042 134.0964 at 20iterations 3.234542 67.06129 at 30iterations 1.856162 38.92987 at 40iterations 1.064973 20.50135 at 50iterations 0.6100253 13.71254 at 60iterations 0.3491700 6.266033 at 70iterations 0.2004514 3.912797 at 80iterations 0.1147968 2.315170 at 90iterations 6.5389141E-02 1.215734 at 100iterations 3.7558842E-02 0.6967468 at 110iterations 2.1393878E-02 0.3957891 at 120iterations 1.2277731E-02 0.2239359 at 130iterations 7.0147035E-03 0.1312695 at 140iterations 4.0121777E-03 7.6324463E-02 at 150iterations 2.2939760E-03 4.2327881E-02 at 160iterations 1.3142512E-03 2.2550106E-02 at 170iterations 7.5420178E-04 1.4827728E-02 at 180iterations finished qdiffx linear iterations at : 20:25:43 total time elapsed so far: 10.90000 # loops : 180 mean,max change (kT/e) : 7.5420178E-04 1.4827728E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 20:25:43 11.070u 0.176s 0:11.52 97.5% 0+0k 0+0io 0pf+0w