Wed Feb 15 08:56:12 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_thinner.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 15 2012 at 08:56:13 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 = 3471 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: 0.5727432 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): -3.077000 48.55300 ymin,ymax (A): -13.31000 48.84700 zmin,zma (A): -4.799000 56.66900 x,y,z range (A): 51.63000 62.15700 61.46800 scale (grids/A): 0.5727432 object centre (A): 22.73800 17.76850 25.93500 number of atom coordinates read : 3471 total number of charged atoms : 3332 net assigned charge : 1.4662743E-05 assigned positive charge : 533.7770 centred at (gu) : 91.33139 88.91510 87.96011 assigned negative charge : -533.7784 centred at (gu) : 91.25562 88.96780 87.94171 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7350 nv = 96 ne = 84 npr = 70115 no. pairs analyzed = 70115 no. exposed pairs = 4479 no. arc points = 31719 no. surface atoms = 1505 nbur = 1966 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 = 1.512000 m= 299 mr = 3760 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3289 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9637 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6822503E-10 2.1553036E-10 midg,1,midg; midg,igrid,midg 1.3648072E-09 -8.6114110E-10 1,midg,midg; igrid,midg,midg -1.1623886E-09 2.0949682E-09 gauss-seidel spectral radius is 0.9843081 estimated iterations to convergence 66 setup time was (sec) 0.6900000 now iterating at: 08:56:14 rms-change max change #iterations 0.1009906 17.32777 at 10iterations 7.5780861E-03 1.364717 at 20iterations 5.9919129E-04 8.1352234E-02 at 30iterations 6.2009123E-05 8.3484650E-03 at 40iterations 1.0168809E-05 1.4533997E-03 at 50iterations finished qdiffx linear iterations at : 08:56:17 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 1.0168809E-05 1.4533997E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 08:56:17 3.756u 0.188s 0:04.38 89.7% 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 Wed Feb 15 2012 at 08:56:17 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 = 3471 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: 1.718230 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): -3.077000 48.55300 ymin,ymax (A): -13.31000 48.84700 zmin,zma (A): -4.799000 56.66900 x,y,z range (A): 51.63000 62.15700 61.46800 scale (grids/A): 1.718230 object centre (A): 22.73800 17.76850 25.93500 number of atom coordinates read : 3471 total number of charged atoms : 3332 net assigned charge : 1.4662743E-05 assigned positive charge : 533.7770 centred at (gu) : 93.99320 86.74438 83.87923 assigned negative charge : -533.7784 centred at (gu) : 93.76624 86.90305 83.82463 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 80555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31719 grid for indexing accessible points = 1.400000 m= 26158 mr = 53767 m= 2894 mr = 18323 m= 97 mr = 1484 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 554 time to turn everything in is 0.6300000 number of dielectric boundary points 36116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 356 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 25782 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) : 0.5727432 object centre at (A) : 22.73800 17.76850 25.93500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6520983E-02 1.4170492E-02 midg,1,midg; midg,igrid,midg 9.0482049E-03 -2.2971616E-03 1,midg,midg; igrid,midg,midg 2.0158410E-03 1.2797584E-03 gauss-seidel spectral radius is 0.9984072 estimated iterations to convergence 199 setup time was (sec) 0.9500000 now iterating at: 08:56:18 rms-change max change #iterations 4.117924 178.6206 at 10iterations 1.805829 68.29052 at 20iterations 0.7958806 25.94066 at 30iterations 0.3514170 11.86401 at 40iterations 0.1549630 5.490912 at 50iterations 6.8027742E-02 2.350756 at 60iterations 3.0056544E-02 1.004070 at 70iterations 1.3229270E-02 0.4385910 at 80iterations 5.8214008E-03 0.1961098 at 90iterations 2.5689597E-03 7.5290680E-02 at 100iterations 1.1334398E-03 3.5391808E-02 at 110iterations 4.9868197E-04 1.5462875E-02 at 120iterations finished qdiffx linear iterations at : 08:56:26 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 4.9868197E-04 1.5462875E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 08:56:26 8.258u 0.269s 0:09.02 94.3% 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 15 2012 at 08:56:26 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 = 3471 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.577344 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): -3.077000 48.55300 ymin,ymax (A): -13.31000 48.84700 zmin,zma (A): -4.799000 56.66900 x,y,z range (A): 51.63000 62.15700 61.46800 scale (grids/A): 2.577344 object centre (A): 22.73800 17.76850 25.93500 number of atom coordinates read : 3471 total number of charged atoms : 3332 net assigned charge : 1.4662743E-05 assigned positive charge : 533.7770 centred at (gu) : 95.98936 85.11626 80.81860 assigned negative charge : -533.7784 centred at (gu) : 95.64925 85.35442 80.73692 start vw surface at 0.2400000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 186489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31719 grid for indexing accessible points = 1.400000 m= 88609 mr = 131295 m= 26949 mr = 70244 m= 4570 mr = 20644 m= 406 mr = 3089 m= 9 mr = 218 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 1876 time to turn everything in is 1.690000 number of dielectric boundary points 81543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 26647 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) : 1.718230 object centre at (A) : 22.73800 17.76850 25.93500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2594349 0.2120703 midg,1,midg; midg,igrid,midg 0.1581542 3.7162378E-02 1,midg,midg; igrid,midg,midg -5.3197369E-03 -2.6927337E-02 gauss-seidel spectral radius is 0.9992173 estimated iterations to convergence 282 setup time was (sec) 2.000000 now iterating at: 08:56:29 rms-change max change #iterations 10.30126 364.3929 at 10iterations 5.957747 139.0889 at 20iterations 3.413613 76.94601 at 30iterations 1.952792 47.83283 at 40iterations 1.115687 23.33148 at 50iterations 0.6339300 12.41596 at 60iterations 0.3604430 7.144947 at 70iterations 0.2046057 4.008497 at 80iterations 0.1161168 2.631751 at 90iterations 6.5697350E-02 1.215260 at 100iterations 3.7264481E-02 0.7081370 at 110iterations 2.1063183E-02 0.4118862 at 120iterations 1.1925597E-02 0.2266283 at 130iterations 6.7353332E-03 0.1257396 at 140iterations 3.8114879E-03 7.3224068E-02 at 150iterations 2.1559328E-03 3.9411545E-02 at 160iterations 1.2215622E-03 2.2413731E-02 at 170iterations 6.8992167E-04 1.2651920E-02 at 180iterations finished qdiffx linear iterations at : 08:56:42 total time elapsed so far: 15.15000 # loops : 180 mean,max change (kT/e) : 6.8992167E-04 1.2651920E-02 energy calculations done at 15.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 08:56:43 15.352u 0.280s 0:16.56 94.3% 0+0k 0+0io 0pf+0w