Sun Oct 9 11:36:44 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 Sun Oct 9 2011 at 11:36:44 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 = 2032 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: 0.6311162 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): -6.098000 38.88100 ymin,ymax (A): 5.456000 61.86400 zmin,zma (A): -15.46600 29.33400 x,y,z range (A): 44.97900 56.40800 44.80000 scale (grids/A): 0.6311162 object centre (A): 16.39150 33.66000 6.934000 number of atom coordinates read : 2032 total number of charged atoms : 1894 net assigned charge : 6.4820051E-06 assigned positive charge : 289.3238 centred at (gu) : 89.35957 92.77002 91.74485 assigned negative charge : -289.3243 centred at (gu) : 89.55589 92.70562 91.66920 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5593 nv = 96 ne = 84 npr = 40831 no. pairs analyzed = 40831 no. exposed pairs = 2878 no. arc points = 19937 no. surface atoms = 960 nbur = 1072 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 2736 m= 4 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1904 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6537 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7143593E-09 6.9859434E-09 midg,1,midg; midg,igrid,midg -2.5586320E-09 7.4311948E-09 1,midg,midg; igrid,midg,midg 1.4524844E-08 -1.1983004E-08 gauss-seidel spectral radius is 0.9869565 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 11:36:45 rms-change max change #iterations 0.1117859 18.48510 at 10iterations 1.0585727E-02 1.833389 at 20iterations 1.0092880E-03 0.1614666 at 30iterations 9.6149270E-05 1.6334534E-02 at 40iterations 9.6471858E-06 1.7423630E-03 at 50iterations finished qdiffx linear iterations at : 11:36:48 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 9.6471858E-06 1.7423630E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 11:36:48 3.445u 0.193s 0:03.91 92.8% 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 Sun Oct 9 2011 at 11:36:48 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 = 2032 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: 1.893348 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): -6.098000 38.88100 ymin,ymax (A): 5.456000 61.86400 zmin,zma (A): -15.46600 29.33400 x,y,z range (A): 44.97900 56.40800 44.80000 scale (grids/A): 1.893348 object centre (A): 16.39150 33.66000 6.934000 number of atom coordinates read : 2032 total number of charged atoms : 1894 net assigned charge : 6.4820051E-06 assigned positive charge : 289.3238 centred at (gu) : 88.07853 98.30998 95.23438 assigned negative charge : -289.3243 centred at (gu) : 88.66782 98.11713 95.00777 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19937 grid for indexing accessible points = 1.400000 m= 20875 mr = 38984 m= 3547 mr = 14401 m= 228 mr = 2170 m= 5 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 28805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14926 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) : 0.6311162 object centre at (A) : 16.39150 33.66000 6.934000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2835345E-03 6.3924124E-03 midg,1,midg; midg,igrid,midg 3.1481714E-03 2.5410894E-02 1,midg,midg; igrid,midg,midg 1.2064960E-02 -1.7190885E-02 gauss-seidel spectral radius is 0.9985722 estimated iterations to convergence 210 setup time was (sec) 0.7500000 now iterating at: 11:36:49 rms-change max change #iterations 3.532530 185.0040 at 10iterations 1.619334 74.14365 at 20iterations 0.7483094 27.20955 at 30iterations 0.3435654 13.47789 at 40iterations 0.1583707 5.960119 at 50iterations 7.2932653E-02 2.555364 at 60iterations 3.3521552E-02 1.109292 at 70iterations 1.5408088E-02 0.5328979 at 80iterations 7.1074800E-03 0.2877636 at 90iterations 3.2561771E-03 0.1171141 at 100iterations 1.5010504E-03 5.9032440E-02 at 110iterations 6.9154712E-04 2.3988724E-02 at 120iterations finished qdiffx linear iterations at : 11:36:56 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 6.9154712E-04 2.3988724E-02 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 11:36:56 7.329u 0.230s 0:07.85 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 Sun Oct 9 2011 at 11:36:56 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 = 2032 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.840023 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): -6.098000 38.88100 ymin,ymax (A): 5.456000 61.86400 zmin,zma (A): -15.46600 29.33400 x,y,z range (A): 44.97900 56.40800 44.80000 scale (grids/A): 2.840023 object centre (A): 16.39150 33.66000 6.934000 number of atom coordinates read : 2032 total number of charged atoms : 1894 net assigned charge : 6.4820051E-06 assigned positive charge : 289.3238 centred at (gu) : 87.11781 102.4649 97.85145 assigned negative charge : -289.3243 centred at (gu) : 88.00170 102.1759 97.51178 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 138220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19937 grid for indexing accessible points = 1.400000 m= 66180 mr = 95567 m= 24581 mr = 51646 m= 6364 mr = 19107 m= 919 mr = 4644 m= 50 mr = 539 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 64800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 15151 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) : 1.893348 object centre at (A) : 16.39150 33.66000 6.934000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4983353E-02 8.5146584E-02 midg,1,midg; midg,igrid,midg 4.2763878E-02 0.2499538 1,midg,midg; igrid,midg,midg 7.3575325E-02 -0.1678362 gauss-seidel spectral radius is 0.9992436 estimated iterations to convergence 287 setup time was (sec) 1.440000 now iterating at: 11:36:58 rms-change max change #iterations 8.532908 354.3921 at 10iterations 5.022282 127.4851 at 20iterations 2.930702 69.76279 at 30iterations 1.698617 41.24884 at 40iterations 0.9833317 21.19117 at 50iterations 0.5653701 11.27011 at 60iterations 0.3250292 7.222281 at 70iterations 0.1868652 4.008847 at 80iterations 0.1067149 2.192863 at 90iterations 6.1168063E-02 1.251167 at 100iterations 3.5052113E-02 0.6803589 at 110iterations 1.9952152E-02 0.3913956 at 120iterations 1.1417164E-02 0.2378635 at 130iterations 6.5304320E-03 0.1464806 at 140iterations 3.7385901E-03 7.2923660E-02 at 150iterations 2.1309487E-03 4.2148590E-02 at 160iterations 1.2179875E-03 2.4786949E-02 at 170iterations 6.9519138E-04 1.4272928E-02 at 180iterations finished qdiffx linear iterations at : 11:37:08 total time elapsed so far: 11.60000 # loops : 180 mean,max change (kT/e) : 6.9519138E-04 1.4272928E-02 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.77000 DelPhi exited at 11:37:08 11.774u 0.210s 0:12.26 97.7% 0+0k 0+0io 0pf+0w