Sun Oct 9 03:54:01 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 03:54:01 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4712 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4029884 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): -2.359000 79.08000 ymin,ymax (A): -12.12600 56.42000 zmin,zma (A): -15.59200 72.74800 x,y,z range (A): 81.43900 68.54601 88.34000 scale (grids/A): 0.4029884 object centre (A): 38.36050 22.14700 28.57800 number of atom coordinates read : 4712 total number of charged atoms : 4395 net assigned charge : 20.30001 assigned positive charge : 688.6090 centred at (gu) : 86.14008 91.85429 83.33131 assigned negative charge : -668.3140 centred at (gu) : 85.99974 91.90417 83.22136 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 4452 nv = 96 ne = 84 npr = 94005 no. pairs analyzed = 94005 no. exposed pairs = 6221 no. arc points = 44520 no. surface atoms = 2081 nbur = 2631 mkacc time = 0.2100000 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 = 2.072000 m= 110 mr = 1920 m= 0 mr = 1 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 2641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3225 ## 839 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 6100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5838082E-13 1.7058899E-13 midg,1,midg; midg,igrid,midg 5.6101147E-13 6.9220091E-13 1,midg,midg; igrid,midg,midg -8.7412217E-13 4.5796239E-13 gauss-seidel spectral radius is 0.9686872 estimated iterations to convergence 47 setup time was (sec) 0.6600000 now iterating at: 03:54:02 rms-change max change #iterations 1.9563036E-02 3.689976 at 10iterations 2.0779064E-03 0.5285797 at 20iterations 4.3365278E-04 0.1030617 at 30iterations 9.2200775E-05 2.0618439E-02 at 40iterations 1.9659386E-05 4.2228699E-03 at 50iterations finished qdiffx linear iterations at : 03:54:04 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.9659386E-05 4.2228699E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:54:05 3.427u 0.172s 0:03.91 91.8% 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 03:54:05 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4712 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.208965 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): -2.359000 79.08000 ymin,ymax (A): -12.12600 56.42000 zmin,zma (A): -15.59200 72.74800 x,y,z range (A): 81.43900 68.54601 88.34000 scale (grids/A): 1.208965 object centre (A): 38.36050 22.14700 28.57800 number of atom coordinates read : 4712 total number of charged atoms : 4395 net assigned charge : 20.30001 assigned positive charge : 688.6090 centred at (gu) : 78.41876 95.56139 69.99226 assigned negative charge : -668.3140 centred at (gu) : 77.99906 95.71255 69.66410 start vw surface at 0.2100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 53276 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44520 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.932000 m= 10244 mr = 33355 m= 384 mr = 5387 m= 0 mr = 37 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 461 time to turn everything in is 0.4700000 number of dielectric boundary points 25125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 901 ## 47 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 29328 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) : 0.4029884 object centre at (A) : 38.36050 22.14700 28.57800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9086771E-03 1.3988375E-03 midg,1,midg; midg,igrid,midg 1.5725255E-03 1.5168081E-03 1,midg,midg; igrid,midg,midg -4.1135738E-04 9.5920108E-04 gauss-seidel spectral radius is 0.9966946 estimated iterations to convergence 139 setup time was (sec) 0.7400000 now iterating at: 03:54:06 rms-change max change #iterations 1.967900 103.0564 at 10iterations 0.6028053 29.12796 at 20iterations 0.1855657 9.173195 at 30iterations 5.7931665E-02 2.691446 at 40iterations 1.8545216E-02 0.8200493 at 50iterations 6.3201170E-03 0.2767639 at 60iterations 2.5533417E-03 0.1106052 at 70iterations 1.2418791E-03 4.9129486E-02 at 80iterations 6.8008149E-04 2.6004791E-02 at 90iterations 3.9103531E-04 1.3679504E-02 at 100iterations 2.2857919E-04 7.9813004E-03 at 110iterations 1.3419930E-04 4.6834946E-03 at 120iterations finished qdiffx linear iterations at : 03:54:12 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 1.3419930E-04 4.6834946E-03 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 03:54:12 6.913u 0.180s 0:07.39 95.9% 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 03:54:12 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4712 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.813448 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): -2.359000 79.08000 ymin,ymax (A): -12.12600 56.42000 zmin,zma (A): -15.59200 72.74800 x,y,z range (A): 81.43900 68.54601 88.34000 scale (grids/A): 1.813448 object centre (A): 38.36050 22.14700 28.57800 number of atom coordinates read : 4712 total number of charged atoms : 4395 net assigned charge : 20.30001 assigned positive charge : 688.6090 centred at (gu) : 72.62771 98.34180 59.98806 assigned negative charge : -668.3140 centred at (gu) : 71.99863 98.56883 59.49612 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 125709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44520 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.932000 m= 42079 mr = 84446 m= 5712 mr = 29237 m= 281 mr = 3111 m= 6 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1537 time to turn everything in is 0.9500000 number of dielectric boundary points 56926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 34360 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) : 1.208965 object centre at (A) : 38.36050 22.14700 28.57800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3701264 1.9909237E-02 midg,1,midg; midg,igrid,midg 3.7895065E-02 2.8264299E-02 1,midg,midg; igrid,midg,midg 1.0174334E-02 1.6627681E-02 gauss-seidel spectral radius is 0.9985723 estimated iterations to convergence 210 setup time was (sec) 1.240000 now iterating at: 03:54:14 rms-change max change #iterations 6.205558 218.0907 at 10iterations 2.961240 92.58324 at 20iterations 1.402294 40.25349 at 30iterations 0.6624873 18.81028 at 40iterations 0.3100986 8.729084 at 50iterations 0.1447223 3.945707 at 60iterations 6.7621164E-02 1.790407 at 70iterations 3.1584159E-02 0.8070717 at 80iterations 1.4923690E-02 0.4271212 at 90iterations 7.1578706E-03 0.2037506 at 100iterations 3.5279291E-03 9.1659546E-02 at 110iterations 1.8363146E-03 4.8252106E-02 at 120iterations 1.0339408E-03 2.7683258E-02 at 130iterations 6.2883308E-04 1.5332103E-02 at 140iterations 4.0529689E-04 9.3708038E-03 at 150iterations 2.7114674E-04 5.9928894E-03 at 160iterations 1.8551633E-04 3.9768219E-03 at 170iterations 1.2785627E-04 2.6473999E-03 at 180iterations finished qdiffx linear iterations at : 03:54:25 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 1.2785627E-04 2.6473999E-03 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 03:54:25 12.296u 0.221s 0:12.79 97.8% 0+0k 0+0io 0pf+0w