Tue Oct 11 05:27:25 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 Tue Oct 11 2011 at 05:27:25 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7034461 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): 25.63900 72.17700 ymin,ymax (A): -20.38200 30.22600 zmin,zma (A): 3.985000 46.58200 x,y,z range (A): 46.53800 50.60800 42.59700 scale (grids/A): 0.7034461 object centre (A): 48.90800 4.922000 25.28350 number of atom coordinates read : 2054 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 88.98758 90.85896 90.07415 assigned negative charge : -305.0792 centred at (gu) : 89.09137 90.78419 90.16255 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6855 nv = 96 ne = 84 npr = 41335 no. pairs analyzed = 41335 no. exposed pairs = 2472 no. arc points = 16979 no. surface atoms = 839 nbur = 1215 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 3940 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1610 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7690 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6491923E-08 9.7638893E-09 midg,1,midg; midg,igrid,midg 1.3724517E-08 9.6702365E-08 1,midg,midg; igrid,midg,midg 1.1509440E-07 2.7275837E-09 gauss-seidel spectral radius is 0.9894642 estimated iterations to convergence 79 setup time was (sec) 0.3500000 now iterating at: 05:27:26 rms-change max change #iterations 0.1917411 24.06882 at 10iterations 2.3426441E-02 3.010523 at 20iterations 3.0050592E-03 0.3797798 at 30iterations 4.5364082E-04 6.2553406E-02 at 40iterations 9.9080775E-05 1.2880325E-02 at 50iterations finished qdiffx linear iterations at : 05:27:28 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 9.9080775E-05 1.2880325E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 05:27:29 3.342u 0.174s 0:03.98 88.1% 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 Tue Oct 11 2011 at 05:27:29 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 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: 2.110338 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): 25.63900 72.17700 ymin,ymax (A): -20.38200 30.22600 zmin,zma (A): 3.985000 46.58200 x,y,z range (A): 46.53800 50.60800 42.59700 scale (grids/A): 2.110338 object centre (A): 48.90800 4.922000 25.28350 number of atom coordinates read : 2054 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 86.96300 92.57676 90.22231 assigned negative charge : -305.0792 centred at (gu) : 87.27422 92.35288 90.48771 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72988 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 29786 mr = 51854 m= 5690 mr = 22820 m= 498 mr = 3846 m= 20 mr = 236 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 30224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15279 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) : 0.7034461 object centre at (A) : 48.90800 4.922000 25.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8434182E-02 2.5129717E-02 midg,1,midg; midg,igrid,midg 3.3017442E-02 3.6814831E-02 1,midg,midg; igrid,midg,midg 4.1374050E-02 -3.5066660E-02 gauss-seidel spectral radius is 0.9988158 estimated iterations to convergence 230 setup time was (sec) 0.6000000 now iterating at: 05:27:30 rms-change max change #iterations 4.501237 215.6073 at 10iterations 2.211582 79.79085 at 20iterations 1.091279 37.70218 at 30iterations 0.5397784 16.34604 at 40iterations 0.2676161 8.338040 at 50iterations 0.1320238 4.119614 at 60iterations 6.5117009E-02 2.084554 at 70iterations 3.2335255E-02 1.015287 at 80iterations 1.6063908E-02 0.4619350 at 90iterations 8.0143865E-03 0.2782021 at 100iterations 4.0072324E-03 0.1174202 at 110iterations 2.0511916E-03 6.1695099E-02 at 120iterations finished qdiffx linear iterations at : 05:27:37 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 2.0511916E-03 6.1695099E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 05:27:37 7.909u 0.219s 0:08.42 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 Tue Oct 11 2011 at 05:27:38 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 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: 3.165507 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): 25.63900 72.17700 ymin,ymax (A): -20.38200 30.22600 zmin,zma (A): 3.985000 46.58200 x,y,z range (A): 46.53800 50.60800 42.59700 scale (grids/A): 3.165507 object centre (A): 48.90800 4.922000 25.28350 number of atom coordinates read : 2054 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 85.44441 93.86511 90.33361 assigned negative charge : -305.0792 centred at (gu) : 85.91148 93.52930 90.73164 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 168333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 92403 mr = 125044 m= 37997 mr = 77189 m= 10699 mr = 31454 m= 2035 mr = 8265 m= 215 mr = 1474 m= 10 mr = 124 m= 0 mr = 5 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 68137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 15400 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) : 2.110338 object centre at (A) : 48.90800 4.922000 25.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1934839 0.2218440 midg,1,midg; midg,igrid,midg 0.2442230 0.3220304 1,midg,midg; igrid,midg,midg 0.3830679 -0.4168670 gauss-seidel spectral radius is 0.9992918 estimated iterations to convergence 296 setup time was (sec) 1.380000 now iterating at: 05:27:39 rms-change max change #iterations 10.03862 366.2355 at 10iterations 5.916233 126.7089 at 20iterations 3.480312 66.74812 at 30iterations 2.050510 43.82499 at 40iterations 1.202927 22.18037 at 50iterations 0.7044630 12.62534 at 60iterations 0.4135170 7.600578 at 70iterations 0.2418868 4.629738 at 80iterations 0.1415582 2.600829 at 90iterations 8.2690269E-02 1.510076 at 100iterations 4.8368447E-02 0.9042854 at 110iterations 2.8363926E-02 0.5129623 at 120iterations 1.6636837E-02 0.2913055 at 130iterations 9.8399436E-03 0.1832218 at 140iterations 5.9015369E-03 0.1124878 at 150iterations 3.6055725E-03 6.9915771E-02 at 160iterations 2.2949562E-03 4.1377544E-02 at 170iterations 1.5336004E-03 3.0094147E-02 at 180iterations finished qdiffx linear iterations at : 05:27:50 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 1.5336004E-03 3.0094147E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 05:27:51 12.805u 0.211s 0:13.56 95.9% 0+0k 0+0io 0pf+0w