Sat Oct 8 17:21:07 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 17:21:07 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 = 3477 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5598805 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): -55.57600 8.009000 ymin,ymax (A): 21.20400 82.75600 zmin,zma (A): 41.00600 95.90900 x,y,z range (A): 63.58500 61.55200 54.90300 scale (grids/A): 0.5598805 object centre (A): -23.78350 51.98000 68.45750 number of atom coordinates read : 3477 total number of charged atoms : 3331 net assigned charge : -2.999993 assigned positive charge : 524.0712 centred at (gu) : 92.52622 90.14673 90.20734 assigned negative charge : -527.0728 centred at (gu) : 92.57378 90.11691 90.21600 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7049 nv = 96 ne = 84 npr = 71321 no. pairs analyzed = 71321 no. exposed pairs = 4347 no. arc points = 29624 no. surface atoms = 1464 nbur = 2013 mkacc time = 0.1500000 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 = 1.540000 m= 310 mr = 3792 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3500000 number of dielectric boundary points 3554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3103 ## 383 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9191 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7729715E-10 -4.3119316E-10 midg,1,midg; midg,igrid,midg -6.6258599E-10 9.1292321E-11 1,midg,midg; igrid,midg,midg 1.6603502E-10 -1.7102743E-09 gauss-seidel spectral radius is 0.9835784 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 17:21:08 rms-change max change #iterations 8.7472297E-02 14.68559 at 10iterations 6.3957158E-03 1.057745 at 20iterations 5.4293656E-04 8.7567806E-02 at 30iterations 9.2927134E-05 1.7404556E-02 at 40iterations 2.4791867E-05 4.8666000E-03 at 50iterations finished qdiffx linear iterations at : 17:21:10 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.4791867E-05 4.8666000E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 17:21:11 3.418u 0.174s 0:03.90 91.7% 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 17:21:11 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 = 3477 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.679641 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): -55.57600 8.009000 ymin,ymax (A): 21.20400 82.75600 zmin,zma (A): 41.00600 95.90900 x,y,z range (A): 63.58500 61.55200 54.90300 scale (grids/A): 1.679641 object centre (A): -23.78350 51.98000 68.45750 number of atom coordinates read : 3477 total number of charged atoms : 3331 net assigned charge : -2.999993 assigned positive charge : 524.0712 centred at (gu) : 97.57750 90.43913 90.62101 assigned negative charge : -527.0728 centred at (gu) : 97.72089 90.35079 90.64747 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29624 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25505 mr = 53825 m= 2945 mr = 17941 m= 92 mr = 1446 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 232 time to turn everything in is 0.5600000 number of dielectric boundary points 33044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 323 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25684 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) : 0.5598805 object centre at (A) : -23.78350 51.98000 68.45750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5400603E-03 -1.2413423E-02 midg,1,midg; midg,igrid,midg -2.0789424E-02 3.2936193E-03 1,midg,midg; igrid,midg,midg 1.0767114E-02 -1.3146359E-02 gauss-seidel spectral radius is 0.9983284 estimated iterations to convergence 194 setup time was (sec) 0.8400000 now iterating at: 17:21:12 rms-change max change #iterations 3.867771 174.4562 at 10iterations 1.668077 67.22592 at 20iterations 0.7190772 23.55898 at 30iterations 0.3111912 9.721582 at 40iterations 0.1349846 4.615623 at 50iterations 5.8281943E-02 1.869807 at 60iterations 2.5256144E-02 0.7638378 at 70iterations 1.0943731E-02 0.3600426 at 80iterations 4.7446694E-03 0.1546278 at 90iterations 2.0668469E-03 7.4111938E-02 at 100iterations 9.0484822E-04 3.2550812E-02 at 110iterations 4.0137113E-04 1.3294220E-02 at 120iterations finished qdiffx linear iterations at : 17:21:18 total time elapsed so far: 6.940000 # loops : 120 mean,max change (kT/e) : 4.0137113E-04 1.3294220E-02 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 17:21:19 7.117u 0.212s 0:07.64 95.8% 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 17:21:19 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 = 3477 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: 2.519462 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): -55.57600 8.009000 ymin,ymax (A): 21.20400 82.75600 zmin,zma (A): 41.00600 95.90900 x,y,z range (A): 63.58500 61.55200 54.90300 scale (grids/A): 2.519462 object centre (A): -23.78350 51.98000 68.45750 number of atom coordinates read : 3477 total number of charged atoms : 3331 net assigned charge : -2.999993 assigned positive charge : 524.0712 centred at (gu) : 101.3661 90.65853 90.93127 assigned negative charge : -527.0728 centred at (gu) : 101.5811 90.52583 90.97112 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 180335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29624 grid for indexing accessible points = 1.400000 m= 86847 mr = 131401 m= 26414 mr = 69361 m= 4599 mr = 20093 m= 367 mr = 2994 m= 7 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 709 time to turn everything in is 1.320000 number of dielectric boundary points 74582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 26636 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) : 1.679641 object centre at (A) : -23.78350 51.98000 68.45750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6447660E-02 -0.1468951 midg,1,midg; midg,igrid,midg -0.2230293 9.8618351E-02 1,midg,midg; igrid,midg,midg 3.4366380E-02 -0.2439749 gauss-seidel spectral radius is 0.9991878 estimated iterations to convergence 277 setup time was (sec) 1.610000 now iterating at: 17:21:20 rms-change max change #iterations 9.823532 324.8587 at 10iterations 5.619333 142.0270 at 20iterations 3.202399 68.74790 at 30iterations 1.815614 34.57389 at 40iterations 1.027466 21.84146 at 50iterations 0.5781981 10.95223 at 60iterations 0.3256683 6.279474 at 70iterations 0.1830588 3.449516 at 80iterations 0.1026371 1.877573 at 90iterations 5.7585027E-02 1.039528 at 100iterations 3.2302499E-02 0.6104507 at 110iterations 1.8147286E-02 0.3957939 at 120iterations 1.0153854E-02 0.1722512 at 130iterations 5.7085711E-03 0.1097765 at 140iterations 3.2051783E-03 6.0321376E-02 at 150iterations 1.8121086E-03 3.5567284E-02 at 160iterations 1.0279772E-03 2.0664215E-02 at 170iterations 5.9059769E-04 1.0803223E-02 at 180iterations finished qdiffx linear iterations at : 17:21:30 total time elapsed so far: 11.40000 # loops : 180 mean,max change (kT/e) : 5.9059769E-04 1.0803223E-02 energy calculations done at 11.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 17:21:31 11.566u 0.243s 0:12.08 97.6% 0+0k 0+0io 0pf+0w