Tue Oct 11 08:01:28 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 08:01:28 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6194213 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): -22.07000 29.04900 ymin,ymax (A): 12.28100 63.85600 zmin,zma (A): -9.915999 47.55700 x,y,z range (A): 51.11900 51.57500 57.47300 scale (grids/A): 0.6194213 object centre (A): 3.489500 38.06850 18.82050 number of atom coordinates read : 2825 total number of charged atoms : 2656 net assigned charge : 7.000021 assigned positive charge : 416.4794 centred at (gu) : 90.57597 89.67683 91.35635 assigned negative charge : -409.4804 centred at (gu) : 90.67107 89.66669 91.52787 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7275 nv = 96 ne = 84 npr = 56101 no. pairs analyzed = 56101 no. exposed pairs = 3777 no. arc points = 26597 no. surface atoms = 1275 nbur = 1550 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 333 mr = 3709 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2625 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8850 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2879075E-08 -8.6433563E-09 midg,1,midg; midg,igrid,midg 5.4244245E-09 6.0283685E-09 1,midg,midg; igrid,midg,midg 1.0786834E-08 -1.0080630E-09 gauss-seidel spectral radius is 0.9865314 estimated iterations to convergence 71 setup time was (sec) 0.5900000 now iterating at: 08:01:29 rms-change max change #iterations 0.1285751 19.70799 at 10iterations 1.1540749E-02 1.667282 at 20iterations 1.0651668E-03 0.1545639 at 30iterations 9.8561351E-05 1.4434814E-02 at 40iterations 9.3078579E-06 1.2054443E-03 at 50iterations finished qdiffx linear iterations at : 08:01:32 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 9.3078579E-06 1.2054443E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 08:01:33 3.531u 0.181s 0:04.20 88.3% 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 08:01:33 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.858264 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): -22.07000 29.04900 ymin,ymax (A): 12.28100 63.85600 zmin,zma (A): -9.915999 47.55700 x,y,z range (A): 51.11900 51.57500 57.47300 scale (grids/A): 1.858264 object centre (A): 3.489500 38.06850 18.82050 number of atom coordinates read : 2825 total number of charged atoms : 2656 net assigned charge : 7.000021 assigned positive charge : 416.4794 centred at (gu) : 91.72711 89.03013 94.06832 assigned negative charge : -409.4804 centred at (gu) : 92.01315 88.99985 94.58364 start vw surface at 0.2400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 78648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26597 grid for indexing accessible points = 1.400000 m= 25305 mr = 52408 m= 3277 mr = 17492 m= 163 mr = 1731 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 35727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20830 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) : 0.6194213 object centre at (A) : 3.489500 38.06850 18.82050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7653321E-02 5.9443903E-03 midg,1,midg; midg,igrid,midg 5.8882362E-03 1.0603068E-02 1,midg,midg; igrid,midg,midg -1.5608978E-03 -8.2265874E-03 gauss-seidel spectral radius is 0.9985995 estimated iterations to convergence 212 setup time was (sec) 0.9800000 now iterating at: 08:01:34 rms-change max change #iterations 4.164743 157.7018 at 10iterations 1.920384 65.13685 at 20iterations 0.8856924 28.20484 at 30iterations 0.4099064 12.76581 at 40iterations 0.1906121 6.283428 at 50iterations 8.8019617E-02 2.919041 at 60iterations 4.0666245E-02 1.245037 at 70iterations 1.8818885E-02 0.6193714 at 80iterations 8.7394081E-03 0.2891140 at 90iterations 4.0502292E-03 0.1317816 at 100iterations 1.8718920E-03 5.5747986E-02 at 110iterations 8.6904952E-04 2.8226852E-02 at 120iterations finished qdiffx linear iterations at : 08:01:41 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 8.6904952E-04 2.8226852E-02 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 08:01:42 8.451u 0.219s 0:09.24 93.7% 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 Tue Oct 11 2011 at 08:01:42 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.787396 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): -22.07000 29.04900 ymin,ymax (A): 12.28100 63.85600 zmin,zma (A): -9.915999 47.55700 x,y,z range (A): 51.11900 51.57500 57.47300 scale (grids/A): 2.787396 object centre (A): 3.489500 38.06850 18.82050 number of atom coordinates read : 2825 total number of charged atoms : 2656 net assigned charge : 7.000021 assigned positive charge : 416.4794 centred at (gu) : 92.59040 88.54499 96.10218 assigned negative charge : -409.4804 centred at (gu) : 93.01970 88.49966 96.87546 start vw surface at 0.2300000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 182231 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26597 grid for indexing accessible points = 1.400000 m= 84589 mr = 127833 m= 26927 mr = 66890 m= 5514 mr = 20464 m= 639 mr = 3668 m= 29 mr = 317 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 80757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 21245 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) : 1.858264 object centre at (A) : 3.489500 38.06850 18.82050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5590807 0.1481917 midg,1,midg; midg,igrid,midg 8.4496200E-02 0.1800801 1,midg,midg; igrid,midg,midg 1.5042158E-02 -2.1764108E-04 gauss-seidel spectral radius is 0.9992646 estimated iterations to convergence 291 setup time was (sec) 1.900000 now iterating at: 08:01:44 rms-change max change #iterations 9.975460 345.9703 at 10iterations 5.886186 167.2749 at 20iterations 3.431286 67.77072 at 30iterations 1.996337 40.59570 at 40iterations 1.155164 21.06204 at 50iterations 0.6690968 13.27782 at 60iterations 0.3859815 7.570431 at 70iterations 0.2231788 4.527420 at 80iterations 0.1284802 2.804870 at 90iterations 7.4000247E-02 1.367103 at 100iterations 4.2649057E-02 0.7507267 at 110iterations 2.4474531E-02 0.4517314 at 120iterations 1.4112096E-02 0.2698746 at 130iterations 8.1180632E-03 0.1560991 at 140iterations 4.6611219E-03 8.5342407E-02 at 150iterations 2.6864309E-03 4.8736334E-02 at 160iterations 1.5412580E-03 2.9353142E-02 at 170iterations 8.8836410E-04 1.8588066E-02 at 180iterations finished qdiffx linear iterations at : 08:01:54 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 8.8836410E-04 1.8588066E-02 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 08:01:55 12.584u 0.231s 0:13.30 96.3% 0+0k 0+0io 0pf+0w