Sun Oct 9 08:43:47 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 Sun Oct 9 2011 at 08:43:47 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5906 !!! WARNING: HIR 702 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5169234 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): 15.14000 84.00900 ymin,ymax (A): 17.79700 84.21200 zmin,zma (A): 1.219000 67.91500 x,y,z range (A): 68.86900 66.41500 66.69600 scale (grids/A): 0.5169234 object centre (A): 49.57450 51.00450 34.56700 number of atom coordinates read : 5906 total number of charged atoms : 5737 net assigned charge : -4.985983 assigned positive charge : 890.3748 centred at (gu) : 90.36796 88.97771 90.51151 assigned negative charge : -895.3687 centred at (gu) : 90.28865 89.06297 90.55998 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10030 nv = 96 ne = 84 npr = 118035 no. pairs analyzed = 118035 no. exposed pairs = 7542 no. arc points = 52185 no. surface atoms = 2519 nbur = 3387 mkacc time = 0.2000000 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 = 1.652000 m= 370 mr = 5199 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 5190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5068 ## 734 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 13417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2892465E-11 -3.4829289E-10 midg,1,midg; midg,igrid,midg 3.4319483E-10 -3.5505679E-10 1,midg,midg; igrid,midg,midg -3.9755718E-10 2.6016647E-10 gauss-seidel spectral radius is 0.9809428 estimated iterations to convergence 60 setup time was (sec) 0.5700000 now iterating at: 08:43:48 rms-change max change #iterations 7.9801783E-02 11.73318 at 10iterations 4.9314303E-03 0.7127838 at 20iterations 6.5863522E-04 0.1373634 at 30iterations 1.9407533E-04 4.0645599E-02 at 40iterations 6.3900028E-05 1.2886047E-02 at 50iterations finished qdiffx linear iterations at : 08:43:51 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 6.3900028E-05 1.2886047E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 08:43:51 3.552u 0.192s 0:04.11 90.9% 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 08:43:51 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5906 !!! WARNING: HIR 702 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: 1.550770 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): 15.14000 84.00900 ymin,ymax (A): 17.79700 84.21200 zmin,zma (A): 1.219000 67.91500 x,y,z range (A): 68.86900 66.41500 66.69600 scale (grids/A): 1.550770 object centre (A): 49.57450 51.00450 34.56700 number of atom coordinates read : 5906 total number of charged atoms : 5737 net assigned charge : -4.985983 assigned positive charge : 890.3748 centred at (gu) : 91.10204 86.93077 91.53244 assigned negative charge : -895.3687 centred at (gu) : 90.86561 87.18839 91.67999 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 112682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52185 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 34074 mr = 77039 m= 3230 mr = 22889 m= 77 mr = 1488 m= 0 mr = 1 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2153 time to turn everything in is 0.5600000 number of dielectric boundary points 48646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 720 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 43366 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) : 0.5169234 object centre at (A) : 49.57450 51.00450 34.56700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0062899E-03 -3.7542518E-02 midg,1,midg; midg,igrid,midg 1.1643062E-02 -1.9896494E-02 1,midg,midg; igrid,midg,midg -2.4939738E-03 1.6587280E-02 gauss-seidel spectral radius is 0.9982708 estimated iterations to convergence 191 setup time was (sec) 0.8000000 now iterating at: 08:43:52 rms-change max change #iterations 4.427757 161.7402 at 10iterations 1.882575 58.16847 at 20iterations 0.8019413 24.13875 at 30iterations 0.3420931 9.859286 at 40iterations 0.1452534 4.080307 at 50iterations 6.2149316E-02 1.888440 at 60iterations 2.6580103E-02 0.7173691 at 70iterations 1.1371228E-02 0.3089222 at 80iterations 4.9081957E-03 0.1358013 at 90iterations 2.1502466E-03 6.8660736E-02 at 100iterations 9.7209174E-04 3.1551361E-02 at 110iterations 4.6300844E-04 1.6952515E-02 at 120iterations finished qdiffx linear iterations at : 08:44:00 total time elapsed so far: 8.830000 # loops : 120 mean,max change (kT/e) : 4.6300844E-04 1.6952515E-02 energy calculations done at 8.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 08:44:01 8.973u 0.255s 0:09.69 95.1% 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 08:44:01 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5906 !!! WARNING: HIR 702 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.326155 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): 15.14000 84.00900 ymin,ymax (A): 17.79700 84.21200 zmin,zma (A): 1.219000 67.91500 x,y,z range (A): 68.86900 66.41500 66.69600 scale (grids/A): 2.326155 object centre (A): 49.57450 51.00450 34.56700 number of atom coordinates read : 5906 total number of charged atoms : 5737 net assigned charge : -4.985983 assigned positive charge : 890.3748 centred at (gu) : 91.65240 85.39552 92.29819 assigned negative charge : -895.3687 centred at (gu) : 91.29829 85.78223 92.51989 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 262132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52185 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 120375 mr = 189302 m= 32336 mr = 93910 m= 4767 mr = 23757 m= 304 mr = 3065 m= 2 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 7511 time to turn everything in is 1.400000 number of dielectric boundary points 109780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 45786 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) : 1.550770 object centre at (A) : 49.57450 51.00450 34.56700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0111161E-02 -0.9428667 midg,1,midg; midg,igrid,midg -7.3113791E-03 -0.3152252 1,midg,midg; igrid,midg,midg 0.2381357 0.4032127 gauss-seidel spectral radius is 0.9992393 estimated iterations to convergence 286 setup time was (sec) 1.680000 now iterating at: 08:44:03 rms-change max change #iterations 11.98910 266.9836 at 10iterations 7.136349 154.7483 at 20iterations 4.190921 94.43124 at 30iterations 2.453355 51.76569 at 40iterations 1.427430 27.33645 at 50iterations 0.8279801 16.31912 at 60iterations 0.4797177 9.200714 at 70iterations 0.2770265 4.865909 at 80iterations 0.1598304 2.879677 at 90iterations 9.1839075E-02 1.693865 at 100iterations 5.2862898E-02 0.8781624 at 110iterations 3.0339930E-02 0.5282536 at 120iterations 1.7413702E-02 0.2949982 at 130iterations 9.9838385E-03 0.1647310 at 140iterations 5.7323077E-03 9.5836401E-02 at 150iterations 3.2986756E-03 5.4845810E-02 at 160iterations 1.8958084E-03 3.3647537E-02 at 170iterations 1.0944797E-03 1.8905640E-02 at 180iterations finished qdiffx linear iterations at : 08:44:15 total time elapsed so far: 13.56000 # loops : 180 mean,max change (kT/e) : 1.0944797E-03 1.8905640E-02 energy calculations done at 13.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 08:44:15 13.700u 0.238s 0:14.31 97.3% 0+0k 0+0io 0pf+0w