Sat Oct 8 11:34:42 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 11:34:42 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 = 4294 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: 0.5854589 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): -25.59300 35.21400 ymin,ymax (A): 37.82200 97.96200 zmin,zma (A): 31.24200 89.56499 x,y,z range (A): 60.80700 60.14000 58.32300 scale (grids/A): 0.5854589 object centre (A): 4.810498 67.89200 60.40350 number of atom coordinates read : 4294 total number of charged atoms : 4148 net assigned charge : -0.9999640 assigned positive charge : 643.7385 centred at (gu) : 90.60064 87.99271 88.58012 assigned negative charge : -644.7416 centred at (gu) : 90.48434 88.14133 88.71016 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9293 nv = 96 ne = 84 npr = 91472 no. pairs analyzed = 91472 no. exposed pairs = 4679 no. arc points = 31765 no. surface atoms = 1599 nbur = 2695 mkacc time = 0.2300000 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= 402 mr = 5492 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 147 time to turn everything in is 0.4500000 number of dielectric boundary points 4156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3341 ## 360 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 12308 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1431611E-09 -3.9462509E-09 midg,1,midg; midg,igrid,midg 8.1844620E-09 -3.9009098E-09 1,midg,midg; igrid,midg,midg -4.3104640E-09 4.4627311E-09 gauss-seidel spectral radius is 0.9850282 estimated iterations to convergence 67 setup time was (sec) 0.7000000 now iterating at: 11:34:43 rms-change max change #iterations 0.1263385 14.83340 at 10iterations 1.0308268E-02 1.408218 at 20iterations 9.7888615E-04 0.1236877 at 30iterations 1.5327695E-04 1.9807816E-02 at 40iterations 4.3144253E-05 5.8438778E-03 at 50iterations finished qdiffx linear iterations at : 11:34:46 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 4.3144253E-05 5.8438778E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 11:34:46 4.194u 0.418s 0:04.90 93.8% 0+0k 0+0io 6pf+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 11:34:47 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 = 4294 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: 1.756377 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): -25.59300 35.21400 ymin,ymax (A): 37.82200 97.96200 zmin,zma (A): 31.24200 89.56499 x,y,z range (A): 60.80700 60.14000 58.32300 scale (grids/A): 1.756377 object centre (A): 4.810498 67.89200 60.40350 number of atom coordinates read : 4294 total number of charged atoms : 4148 net assigned charge : -0.9999640 assigned positive charge : 643.7385 centred at (gu) : 91.80080 83.97686 85.73920 assigned negative charge : -644.7416 centred at (gu) : 91.45263 84.42354 86.12989 start vw surface at 0.1600000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 103229 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31765 grid for indexing accessible points = 1.400000 m= 35404 mr = 75475 m= 4732 mr = 26521 m= 176 mr = 2953 m= 0 mr = 43 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 5488 time to turn everything in is 0.7900000 number of dielectric boundary points 38549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 32231 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) : 0.5854589 object centre at (A) : 4.810498 67.89200 60.40350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0965820E-02 -2.8485259E-02 midg,1,midg; midg,igrid,midg 4.5924183E-02 -7.5207516E-03 1,midg,midg; igrid,midg,midg -1.5243351E-02 3.1757899E-02 gauss-seidel spectral radius is 0.9985384 estimated iterations to convergence 207 setup time was (sec) 1.090000 now iterating at: 11:34:48 rms-change max change #iterations 4.815873 156.3789 at 10iterations 2.196524 61.62266 at 20iterations 1.002284 27.63428 at 30iterations 0.4590012 13.67895 at 40iterations 0.2103702 6.075743 at 50iterations 9.5971473E-02 2.771545 at 60iterations 4.4060245E-02 1.186605 at 70iterations 2.0165469E-02 0.5414066 at 80iterations 9.2542516E-03 0.2429829 at 90iterations 4.2498354E-03 0.1189365 at 100iterations 1.9561625E-03 5.9616089E-02 at 110iterations 9.1486651E-04 2.6311398E-02 at 120iterations finished qdiffx linear iterations at : 11:34:57 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 9.1486651E-04 2.6311398E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 11:34:57 9.837u 0.467s 0:10.90 94.4% 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 11:34:58 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 = 4294 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: 2.634565 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): -25.59300 35.21400 ymin,ymax (A): 37.82200 97.96200 zmin,zma (A): 31.24200 89.56499 x,y,z range (A): 60.80700 60.14000 58.32300 scale (grids/A): 2.634565 object centre (A): 4.810498 67.89200 60.40350 number of atom coordinates read : 4294 total number of charged atoms : 4148 net assigned charge : -0.9999640 assigned positive charge : 643.7385 centred at (gu) : 92.70085 80.96503 83.60835 assigned negative charge : -644.7416 centred at (gu) : 92.17883 81.63525 84.19479 start vw surface at 0.1600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 240216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31765 grid for indexing accessible points = 1.400000 m= 119394 mr = 183095 m= 38915 mr = 99176 m= 8130 mr = 31551 m= 889 mr = 6204 m= 29 mr = 550 m= 0 mr = 7 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 18438 time to turn everything in is 2.050000 number of dielectric boundary points 86990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 33178 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) : 1.756377 object centre at (A) : 4.810498 67.89200 60.40350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8372799 -0.3205016 midg,1,midg; midg,igrid,midg 0.5698778 -0.1209040 1,midg,midg; igrid,midg,midg -0.2586172 0.2531215 gauss-seidel spectral radius is 0.9992554 estimated iterations to convergence 289 setup time was (sec) 2.390000 now iterating at: 11:35:00 rms-change max change #iterations 11.65886 414.8733 at 10iterations 6.804819 143.2424 at 20iterations 3.946535 66.42522 at 30iterations 2.288992 44.91315 at 40iterations 1.319905 25.60965 at 50iterations 0.7631133 12.86398 at 60iterations 0.4392662 7.343148 at 70iterations 0.2532945 3.929134 at 80iterations 0.1458652 2.225937 at 90iterations 8.3852522E-02 1.345154 at 100iterations 4.8170540E-02 0.7877913 at 110iterations 2.7704615E-02 0.4288940 at 120iterations 1.5960397E-02 0.2494392 at 130iterations 9.1987336E-03 0.1450272 at 140iterations 5.3086844E-03 8.8878632E-02 at 150iterations 3.0783301E-03 5.1853180E-02 at 160iterations 1.7965798E-03 2.8183937E-02 at 170iterations 1.0631199E-03 1.7352104E-02 at 180iterations finished qdiffx linear iterations at : 11:35:15 total time elapsed so far: 17.19000 # loops : 180 mean,max change (kT/e) : 1.0631199E-03 1.7352104E-02 energy calculations done at 17.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.36000 DelPhi exited at 11:35:16 17.366u 0.491s 0:18.14 98.4% 0+0k 0+0io 0pf+0w