Mon Oct 10 19:02:03 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 19:02:03 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 !!! WARNING: HIR 241 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5455771 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): 41.25400 106.5060 ymin,ymax (A): 1.799000 54.68000 zmin,zma (A): 1.131000 57.72800 x,y,z range (A): 65.25201 52.88100 56.59700 scale (grids/A): 0.5455771 object centre (A): 73.88000 28.23950 29.42950 number of atom coordinates read : 2780 total number of charged atoms : 2642 net assigned charge : -0.9859811 assigned positive charge : 414.1727 centred at (gu) : 90.99193 89.66339 91.43867 assigned negative charge : -415.1598 centred at (gu) : 90.93252 89.68187 91.49769 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5509 nv = 96 ne = 84 npr = 53171 no. pairs analyzed = 53171 no. exposed pairs = 4184 no. arc points = 29820 no. surface atoms = 1375 nbur = 1405 mkacc time = 0.1700000 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 = 1.568000 m= 273 mr = 2415 m= 0 mr = 13 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2907 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 7053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0749963E-10 -6.0540795E-10 midg,1,midg; midg,igrid,midg 5.8643368E-11 -1.5781620E-10 1,midg,midg; igrid,midg,midg -3.3071990E-10 3.8734274E-10 gauss-seidel spectral radius is 0.9826788 estimated iterations to convergence 63 setup time was (sec) 0.7300000 now iterating at: 19:02:04 rms-change max change #iterations 6.8286121E-02 11.82261 at 10iterations 4.5091342E-03 0.8071709 at 20iterations 3.1972822E-04 7.4872971E-02 at 30iterations 4.0405626E-05 6.1569214E-03 at 40iterations 1.1249808E-05 1.8723011E-03 at 50iterations finished qdiffx linear iterations at : 19:02:08 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 1.1249808E-05 1.8723011E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 19:02:09 4.692u 0.413s 0:05.44 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 Mon Oct 10 2011 at 19:02:09 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 !!! WARNING: HIR 241 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.636731 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): 41.25400 106.5060 ymin,ymax (A): 1.799000 54.68000 zmin,zma (A): 1.131000 57.72800 x,y,z range (A): 65.25201 52.88100 56.59700 scale (grids/A): 1.636731 object centre (A): 73.88000 28.23950 29.42950 number of atom coordinates read : 2780 total number of charged atoms : 2642 net assigned charge : -0.9859811 assigned positive charge : 414.1727 centred at (gu) : 92.97520 88.98943 94.31593 assigned negative charge : -415.1598 centred at (gu) : 92.79768 89.04561 94.49274 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 59602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29820 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18500 mr = 36645 m= 2330 mr = 11839 m= 65 mr = 1119 m= 0 mr = 7 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 30887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 273 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20251 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) : 0.5455771 object centre at (A) : 73.88000 28.23950 29.42950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4216783E-03 -6.4145373E-03 midg,1,midg; midg,igrid,midg -6.0848817E-03 -3.7197049E-03 1,midg,midg; igrid,midg,midg 1.7828550E-03 1.4977659E-02 gauss-seidel spectral radius is 0.9981977 estimated iterations to convergence 187 setup time was (sec) 0.9900000 now iterating at: 19:02:10 rms-change max change #iterations 3.195719 162.8115 at 10iterations 1.333792 58.27065 at 20iterations 0.5527464 21.77402 at 30iterations 0.2298422 9.049767 at 40iterations 9.5786758E-02 3.677413 at 50iterations 3.9840367E-02 1.514016 at 60iterations 1.6689871E-02 0.6110935 at 70iterations 6.9678901E-03 0.2547951 at 80iterations 2.8901184E-03 0.1120729 at 90iterations 1.2131955E-03 4.6400070E-02 at 100iterations 5.1233231E-04 1.9449711E-02 at 110iterations 2.1694064E-04 7.7610016E-03 at 120iterations finished qdiffx linear iterations at : 19:02:20 total time elapsed so far: 10.80000 # loops : 120 mean,max change (kT/e) : 2.1694064E-04 7.7610016E-03 energy calculations done at 10.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.03000 DelPhi exited at 19:02:21 11.034u 0.430s 0:11.87 96.5% 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 Mon Oct 10 2011 at 19:02:21 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 !!! WARNING: HIR 241 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.455097 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): 41.25400 106.5060 ymin,ymax (A): 1.799000 54.68000 zmin,zma (A): 1.131000 57.72800 x,y,z range (A): 65.25201 52.88100 56.59700 scale (grids/A): 2.455097 object centre (A): 73.88000 28.23950 29.42950 number of atom coordinates read : 2780 total number of charged atoms : 2642 net assigned charge : -0.9859811 assigned positive charge : 414.1727 centred at (gu) : 94.46243 88.48413 96.47369 assigned negative charge : -415.1598 centred at (gu) : 94.19644 88.56844 96.73916 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 137812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29820 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61594 mr = 90617 m= 19295 mr = 46039 m= 3717 mr = 13877 m= 295 mr = 2429 m= 5 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.570000 number of dielectric boundary points 69636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 21113 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) : 1.636731 object centre at (A) : 73.88000 28.23950 29.42950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6625136E-02 -0.1163350 midg,1,midg; midg,igrid,midg -9.5268041E-02 -5.9674773E-02 1,midg,midg; igrid,midg,midg 4.4585388E-02 0.2134924 gauss-seidel spectral radius is 0.9991536 estimated iterations to convergence 271 setup time was (sec) 1.930000 now iterating at: 19:02:23 rms-change max change #iterations 8.648181 410.3656 at 10iterations 4.987357 124.0015 at 20iterations 2.847042 74.77837 at 30iterations 1.612416 37.35919 at 40iterations 0.9074488 19.98914 at 50iterations 0.5080492 11.10217 at 60iterations 0.2844850 6.370569 at 70iterations 0.1583239 3.821748 at 80iterations 8.8371396E-02 2.180161 at 90iterations 4.9007419E-02 1.065845 at 100iterations 2.7194912E-02 0.5888424 at 110iterations 1.5113162E-02 0.3235893 at 120iterations 8.3601847E-03 0.1961365 at 130iterations 4.6429392E-03 0.1031618 at 140iterations 2.5682063E-03 6.2012672E-02 at 150iterations 1.4243935E-03 3.0419827E-02 at 160iterations 7.9024176E-04 1.7883301E-02 at 170iterations 4.3906400E-04 1.0722637E-02 at 180iterations finished qdiffx linear iterations at : 19:02:39 total time elapsed so far: 17.60000 # loops : 180 mean,max change (kT/e) : 4.3906400E-04 1.0722637E-02 energy calculations done at 17.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.82000 DelPhi exited at 19:02:39 17.822u 0.455s 0:18.69 97.7% 0+0k 0+0io 0pf+0w