Wed Feb 1 18:03:07 PST 2012 #!/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 Wed Feb 1 2012 at 18:03:07 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2319 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: 0.6219535 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 0.6219535 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2319 total number of charged atoms : 2255 net assigned charge : 3.000001 assigned positive charge : 345.8231 centred at (gu) : 90.19542 88.35288 89.61085 assigned negative charge : -342.8238 centred at (gu) : 90.22377 88.45016 89.66176 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6084 nv = 96 ne = 84 npr = 46019 no. pairs analyzed = 46019 no. exposed pairs = 2980 no. arc points = 20630 no. surface atoms = 1018 nbur = 1301 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 302 mr = 3280 m= 0 mr = 36 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2074 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0719247E-09 -6.6329170E-10 midg,1,midg; midg,igrid,midg 1.2122825E-08 -2.5032147E-09 1,midg,midg; igrid,midg,midg 4.0164694E-09 6.9946793E-10 gauss-seidel spectral radius is 0.9865904 estimated iterations to convergence 71 setup time was (sec) 0.3700000 now iterating at: 18:03:07 rms-change max change #iterations 0.1175106 18.15067 at 10iterations 1.1005742E-02 2.081194 at 20iterations 1.0755828E-03 0.1620102 at 30iterations 1.3212688E-04 2.2277832E-02 at 40iterations 2.6570646E-05 4.8398972E-03 at 50iterations finished qdiffx linear iterations at : 18:03:10 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.6570646E-05 4.8398972E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 18:03:11 3.420u 0.191s 0:04.03 89.5% 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 Wed Feb 1 2012 at 18:03:11 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2319 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: 1.865861 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 1.865861 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2319 total number of charged atoms : 2255 net assigned charge : 3.000001 assigned positive charge : 345.8231 centred at (gu) : 90.58569 85.05785 88.83218 assigned negative charge : -342.8238 centred at (gu) : 90.67140 85.35017 88.98531 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20630 grid for indexing accessible points = 1.400000 m= 23012 mr = 45365 m= 3554 mr = 16665 m= 185 mr = 2241 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 249 time to turn everything in is 0.3300000 number of dielectric boundary points 28233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 17702 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) : 0.6219535 object centre at (A) : 21.54850 7.176000 10.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0690784E-02 -5.3295502E-03 midg,1,midg; midg,igrid,midg 1.9852772E-02 -9.5335901E-04 1,midg,midg; igrid,midg,midg 2.9398086E-03 -3.0285407E-02 gauss-seidel spectral radius is 0.9985528 estimated iterations to convergence 208 setup time was (sec) 0.5700000 now iterating at: 18:03:11 rms-change max change #iterations 3.826764 183.8521 at 10iterations 1.746398 72.60381 at 20iterations 0.8025912 30.01975 at 30iterations 0.3696433 12.34665 at 40iterations 0.1684109 6.162300 at 50iterations 7.7404216E-02 2.487387 at 60iterations 3.5482250E-02 1.282111 at 70iterations 1.6307877E-02 0.5671968 at 80iterations 7.4910629E-03 0.2462330 at 90iterations 3.4446302E-03 0.1090298 at 100iterations 1.5871684E-03 6.1197281E-02 at 110iterations 7.3223672E-04 2.4163246E-02 at 120iterations finished qdiffx linear iterations at : 18:03:19 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 7.3223672E-04 2.4163246E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 18:03:19 7.892u 0.203s 0:08.44 95.8% 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 Wed Feb 1 2012 at 18:03:19 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2319 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: 2.798791 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 2.798791 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2319 total number of charged atoms : 2255 net assigned charge : 3.000001 assigned positive charge : 345.8231 centred at (gu) : 90.87838 82.58682 88.24825 assigned negative charge : -342.8238 centred at (gu) : 91.00710 83.02515 88.47796 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152214 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20630 grid for indexing accessible points = 1.400000 m= 74781 mr = 110179 m= 26721 mr = 60566 m= 6553 mr = 21280 m= 817 mr = 4986 m= 45 mr = 523 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 818 time to turn everything in is 0.8200000 number of dielectric boundary points 63577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 18034 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) : 1.865861 object centre at (A) : 21.54850 7.176000 10.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2098467 -0.1505459 midg,1,midg; midg,igrid,midg 0.1655335 -3.4311969E-02 1,midg,midg; igrid,midg,midg 2.5910590E-02 -0.4674982 gauss-seidel spectral radius is 0.9992352 estimated iterations to convergence 285 setup time was (sec) 1.060000 now iterating at: 18:03:20 rms-change max change #iterations 9.146305 346.5056 at 10iterations 5.339157 126.4912 at 20iterations 3.086190 71.27553 at 30iterations 1.786846 36.11641 at 40iterations 1.028583 22.10399 at 50iterations 0.5901237 12.01531 at 60iterations 0.3388137 6.945199 at 70iterations 0.1940818 3.620947 at 80iterations 0.1109176 2.259109 at 90iterations 6.3479297E-02 1.192123 at 100iterations 3.6237407E-02 0.7313843 at 110iterations 2.0644546E-02 0.4174805 at 120iterations 1.1794669E-02 0.2691050 at 130iterations 6.7369239E-03 0.1299138 at 140iterations 3.8510929E-03 7.6019287E-02 at 150iterations 2.2088331E-03 4.3483257E-02 at 160iterations 1.2687281E-03 2.4620056E-02 at 170iterations 7.3362148E-04 1.4366150E-02 at 180iterations finished qdiffx linear iterations at : 18:03:32 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 7.3362148E-04 1.4366150E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 18:03:33 12.954u 0.219s 0:13.53 97.2% 0+0k 0+0io 0pf+0w