Sat Oct 15 15:07:31 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 15 2011 at 15:07:31 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1165 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7483393 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): -6.410000 32.23100 ymin,ymax (A): 1.263000 39.96200 zmin,zma (A): -1.640000 45.93200 x,y,z range (A): 38.64100 38.69900 47.57200 scale (grids/A): 0.7483393 object centre (A): 12.91050 20.61250 22.14600 number of atom coordinates read : 1165 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 88.54853 89.29693 88.41498 assigned negative charge : -169.8232 centred at (gu) : 88.25765 89.25833 88.47274 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4397 nv = 96 ne = 84 npr = 22714 no. pairs analyzed = 22714 no. exposed pairs = 1499 no. arc points = 10799 no. surface atoms = 504 nbur = 661 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 281 mr = 2253 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.1200000 number of dielectric boundary points 2367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 860 ## 79 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4519 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0670117E-07 6.2009697E-08 midg,1,midg; midg,igrid,midg 1.0601445E-07 1.2569325E-07 1,midg,midg; igrid,midg,midg -9.7151350E-08 2.2804184E-07 gauss-seidel spectral radius is 0.9905958 estimated iterations to convergence 84 setup time was (sec) 0.3100000 now iterating at: 15:07:31 rms-change max change #iterations 0.1858770 29.64776 at 10iterations 2.4879104E-02 4.349833 at 20iterations 3.4037260E-03 0.5659103 at 30iterations 4.5317347E-04 7.6045990E-02 at 40iterations 6.1372419E-05 1.1287689E-02 at 50iterations finished qdiffx linear iterations at : 15:07:34 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.1372419E-05 1.1287689E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 15:07:35 3.307u 0.161s 0:03.75 92.2% 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 15 2011 at 15:07:35 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1165 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.245018 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): -6.410000 32.23100 ymin,ymax (A): 1.263000 39.96200 zmin,zma (A): -1.640000 45.93200 x,y,z range (A): 38.64100 38.69900 47.57200 scale (grids/A): 2.245018 object centre (A): 12.91050 20.61250 22.14600 number of atom coordinates read : 1165 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 85.64565 87.89069 85.24503 assigned negative charge : -169.8232 centred at (gu) : 84.77312 87.77514 85.41839 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 46401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10799 grid for indexing accessible points = 1.400000 m= 17520 mr = 30297 m= 3393 mr = 13105 m= 297 mr = 2326 m= 16 mr = 159 m= 0 mr = 9 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1277 time to turn everything in is 0.2500000 number of dielectric boundary points 21731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8462 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) : 0.7483393 object centre at (A) : 12.91050 20.61250 22.14600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5289835E-02 4.8342417E-03 midg,1,midg; midg,igrid,midg 3.6831237E-02 3.1628802E-02 1,midg,midg; igrid,midg,midg -2.7663445E-02 3.8656406E-02 gauss-seidel spectral radius is 0.9988541 estimated iterations to convergence 234 setup time was (sec) 0.4600000 now iterating at: 15:07:35 rms-change max change #iterations 3.653257 170.7688 at 10iterations 1.822793 81.57082 at 20iterations 0.9082002 33.34262 at 30iterations 0.4535290 20.18291 at 40iterations 0.2247692 7.849790 at 50iterations 0.1126285 4.463032 at 60iterations 5.5598013E-02 2.076244 at 70iterations 2.7765417E-02 1.057548 at 80iterations 1.3868795E-02 0.4933877 at 90iterations 6.8890909E-03 0.2382431 at 100iterations 3.4207543E-03 0.1259584 at 110iterations 1.7015495E-03 6.1485291E-02 at 120iterations finished qdiffx linear iterations at : 15:07:42 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 1.7015495E-03 6.1485291E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 15:07:43 7.531u 0.195s 0:08.22 93.9% 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 Sat Oct 15 2011 at 15:07:43 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1165 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.367527 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): -6.410000 32.23100 ymin,ymax (A): 1.263000 39.96200 zmin,zma (A): -1.640000 45.93200 x,y,z range (A): 38.64100 38.69900 47.57200 scale (grids/A): 3.367527 object centre (A): 12.91050 20.61250 22.14600 number of atom coordinates read : 1165 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 83.46855 86.83610 82.86752 assigned negative charge : -169.8232 centred at (gu) : 82.15971 86.66280 83.12759 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 106804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10799 grid for indexing accessible points = 1.400000 m= 53644 mr = 73498 m= 22187 mr = 43639 m= 6472 mr = 18281 m= 1207 mr = 5145 m= 172 mr = 943 m= 18 mr = 128 m= 0 mr = 14 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 4270 time to turn everything in is 0.7300000 number of dielectric boundary points 48856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 8488 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) : 2.245018 object centre at (A) : 12.91050 20.61250 22.14600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3718141 4.9396183E-02 midg,1,midg; midg,igrid,midg 0.3088191 0.2508271 1,midg,midg; igrid,midg,midg -0.2093511 0.2719510 gauss-seidel spectral radius is 0.9992941 estimated iterations to convergence 297 setup time was (sec) 0.9700000 now iterating at: 15:07:44 rms-change max change #iterations 7.934043 248.2813 at 10iterations 4.628012 126.3071 at 20iterations 2.680105 67.76039 at 30iterations 1.552495 36.79730 at 40iterations 0.9037644 20.22008 at 50iterations 0.5234875 11.42491 at 60iterations 0.3024118 6.098596 at 70iterations 0.1755478 3.825640 at 80iterations 0.1020535 2.095078 at 90iterations 5.9218697E-02 1.394661 at 100iterations 3.4279134E-02 0.7744408 at 110iterations 1.9913115E-02 0.4176788 at 120iterations 1.1511328E-02 0.2382050 at 130iterations 6.7066411E-03 0.1372520 at 140iterations 3.8817166E-03 8.1663132E-02 at 150iterations 2.2547047E-03 5.0035477E-02 at 160iterations 1.3098057E-03 2.7324677E-02 at 170iterations 7.6010294E-04 1.7248154E-02 at 180iterations finished qdiffx linear iterations at : 15:07:55 total time elapsed so far: 11.82000 # loops : 180 mean,max change (kT/e) : 7.6010294E-04 1.7248154E-02 energy calculations done at 11.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 15:07:56 11.951u 0.228s 0:12.55 96.9% 0+0k 0+0io 0pf+0w