Sat Oct 8 21:05:20 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 21:05:20 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 = 2573 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6142273 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): -10.40100 38.58500 ymin,ymax (A): -21.88200 25.13000 zmin,zma (A): -12.48100 45.47800 x,y,z range (A): 48.98600 47.01200 57.95900 scale (grids/A): 0.6142273 object centre (A): 14.09200 1.624000 16.49850 number of atom coordinates read : 2573 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 88.51897 89.12433 89.52975 assigned negative charge : -386.5045 centred at (gu) : 88.40747 89.15822 89.42826 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6289 nv = 96 ne = 84 npr = 53519 no. pairs analyzed = 53519 no. exposed pairs = 3052 no. arc points = 21697 no. surface atoms = 1021 nbur = 1552 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 293 mr = 3454 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.2000000 number of dielectric boundary points 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2208 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7894 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6264525E-09 7.2605846E-09 midg,1,midg; midg,igrid,midg 5.2832072E-09 4.9434440E-10 1,midg,midg; igrid,midg,midg -5.4138987E-09 6.2013967E-09 gauss-seidel spectral radius is 0.9862691 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 21:05:20 rms-change max change #iterations 0.1183412 18.01256 at 10iterations 1.0737489E-02 1.693216 at 20iterations 9.4820285E-04 0.1428719 at 30iterations 9.0209054E-05 1.6965866E-02 at 40iterations 8.7228027E-06 1.5439987E-03 at 50iterations finished qdiffx linear iterations at : 21:05:23 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 8.7228027E-06 1.5439987E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 21:05:24 3.630u 0.213s 0:04.11 93.4% 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 21:05:24 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 = 2573 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.842682 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): -10.40100 38.58500 ymin,ymax (A): -21.88200 25.13000 zmin,zma (A): -12.48100 45.47800 x,y,z range (A): 48.98600 47.01200 57.95900 scale (grids/A): 1.842682 object centre (A): 14.09200 1.624000 16.49850 number of atom coordinates read : 2573 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 85.55621 87.37246 88.58885 assigned negative charge : -386.5045 centred at (gu) : 85.22220 87.47453 88.28439 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21697 grid for indexing accessible points = 1.400000 m= 22989 mr = 47504 m= 3044 mr = 16729 m= 139 mr = 1768 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3816 time to turn everything in is 0.3500000 number of dielectric boundary points 28623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19222 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) : 0.6142273 object centre at (A) : 14.09200 1.624000 16.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6080050E-02 1.7011348E-02 midg,1,midg; midg,igrid,midg 1.1078104E-02 3.3715775E-03 1,midg,midg; igrid,midg,midg -5.7987315E-03 3.3617496E-02 gauss-seidel spectral radius is 0.9985374 estimated iterations to convergence 207 setup time was (sec) 0.5900000 now iterating at: 21:05:25 rms-change max change #iterations 3.918125 179.7248 at 10iterations 1.781833 62.67976 at 20iterations 0.8126341 27.05584 at 30iterations 0.3709276 13.21722 at 40iterations 0.1689844 5.741364 at 50iterations 7.7172667E-02 2.679028 at 60iterations 3.5119381E-02 1.214216 at 70iterations 1.6098673E-02 0.5084591 at 80iterations 7.3277326E-03 0.2792685 at 90iterations 3.3389530E-03 0.1171875 at 100iterations 1.5270213E-03 5.4077387E-02 at 110iterations 6.9610513E-04 2.1503448E-02 at 120iterations finished qdiffx linear iterations at : 21:05:32 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 6.9610513E-04 2.1503448E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 21:05:32 8.135u 0.240s 0:08.69 96.3% 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 Sat Oct 8 2011 at 21:05:32 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 = 2573 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.764023 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): -10.40100 38.58500 ymin,ymax (A): -21.88200 25.13000 zmin,zma (A): -12.48100 45.47800 x,y,z range (A): 48.98600 47.01200 57.95900 scale (grids/A): 2.764023 object centre (A): 14.09200 1.624000 16.49850 number of atom coordinates read : 2573 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 83.33429 86.05850 87.88311 assigned negative charge : -386.5045 centred at (gu) : 82.83327 86.21165 87.42661 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 159016 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21697 grid for indexing accessible points = 1.400000 m= 77245 mr = 115615 m= 25004 mr = 63036 m= 5271 mr = 19755 m= 580 mr = 3802 m= 30 mr = 350 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 12809 time to turn everything in is 0.8800000 number of dielectric boundary points 64574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 19623 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) : 1.842682 object centre at (A) : 14.09200 1.624000 16.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1126509 0.2182530 midg,1,midg; midg,igrid,midg 0.1581906 1.6493961E-02 1,midg,midg; igrid,midg,midg -8.0646664E-02 0.4569324 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 1.150000 now iterating at: 21:05:34 rms-change max change #iterations 9.236142 280.7483 at 10iterations 5.290840 148.2576 at 20iterations 3.000195 68.37634 at 30iterations 1.711464 36.77317 at 40iterations 0.9706212 19.66038 at 50iterations 0.5503864 10.52827 at 60iterations 0.3128011 6.276654 at 70iterations 0.1772743 3.537815 at 80iterations 0.1005435 1.980559 at 90iterations 5.7113886E-02 1.112583 at 100iterations 3.2315269E-02 0.6467018 at 110iterations 1.8269079E-02 0.3422130 at 120iterations 1.0380418E-02 0.2242050 at 130iterations 5.8918516E-03 0.1223912 at 140iterations 3.3360925E-03 6.0993195E-02 at 150iterations 1.8937290E-03 3.7468910E-02 at 160iterations 1.0756333E-03 2.1694183E-02 at 170iterations 6.1119685E-04 1.1449814E-02 at 180iterations finished qdiffx linear iterations at : 21:05:46 total time elapsed so far: 13.59000 # loops : 180 mean,max change (kT/e) : 6.1119685E-04 1.1449814E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.72000 DelPhi exited at 21:05:47 13.726u 0.263s 0:14.25 98.1% 0+0k 0+0io 0pf+0w