Sat Oct 8 16:05:44 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 8 2011 at 16:05:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2332 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6538349 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): -2.409000 45.62100 ymin,ymax (A): -16.93400 29.38100 zmin,zma (A): -17.37000 37.07800 x,y,z range (A): 48.03000 46.31500 54.44800 scale (grids/A): 0.6538349 object centre (A): 21.60600 6.223500 9.853999 number of atom coordinates read : 2332 total number of charged atoms : 2273 net assigned charge : 5.000003 assigned positive charge : 347.8110 centred at (gu) : 90.65485 88.94360 90.21456 assigned negative charge : -342.8117 centred at (gu) : 90.64086 89.08797 90.21731 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6821 nv = 96 ne = 84 npr = 46162 no. pairs analyzed = 46162 no. exposed pairs = 3068 no. arc points = 20978 no. surface atoms = 1038 nbur = 1294 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 3727 m= 0 mr = 52 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1983 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0421197E-08 1.0510793E-08 midg,1,midg; midg,igrid,midg 3.9560121E-08 -8.9599865E-09 1,midg,midg; igrid,midg,midg 7.3676172E-09 1.4355998E-08 gauss-seidel spectral radius is 0.9878570 estimated iterations to convergence 74 setup time was (sec) 0.6400000 now iterating at: 16:05:45 rms-change max change #iterations 0.1493210 26.08047 at 10iterations 1.5276234E-02 2.341335 at 20iterations 1.6293810E-03 0.2126694 at 30iterations 2.0500577E-04 2.5848389E-02 at 40iterations 3.7809477E-05 5.7315826E-03 at 50iterations finished qdiffx linear iterations at : 16:05:49 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 3.7809477E-05 5.7315826E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 16:05:49 4.350u 0.266s 0:04.95 93.1% 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 Sat Oct 8 2011 at 16:05:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2332 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.961505 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): -2.409000 45.62100 ymin,ymax (A): -16.93400 29.38100 zmin,zma (A): -17.37000 37.07800 x,y,z range (A): 48.03000 46.31500 54.44800 scale (grids/A): 1.961505 object centre (A): 21.60600 6.223500 9.853999 number of atom coordinates read : 2332 total number of charged atoms : 2273 net assigned charge : 5.000003 assigned positive charge : 347.8110 centred at (gu) : 91.96413 86.83031 90.64301 assigned negative charge : -342.8117 centred at (gu) : 91.92228 87.26382 90.65188 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72843 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20978 grid for indexing accessible points = 1.400000 m= 26972 mr = 50208 m= 4775 mr = 19786 m= 324 mr = 3164 m= 2 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 300 time to turn everything in is 0.6600000 number of dielectric boundary points 31611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 17931 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) : 0.6538349 object centre at (A) : 21.60600 6.223500 9.853999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2142930E-02 2.0689575E-02 midg,1,midg; midg,igrid,midg 3.0491965E-02 -4.4332724E-03 1,midg,midg; igrid,midg,midg 9.3953300E-04 -3.3513792E-02 gauss-seidel spectral radius is 0.9986889 estimated iterations to convergence 219 setup time was (sec) 1.060000 now iterating at: 16:05:51 rms-change max change #iterations 4.219411 174.0302 at 10iterations 2.007115 64.35817 at 20iterations 0.9544669 33.48526 at 30iterations 0.4557016 15.46023 at 40iterations 0.2164703 6.724776 at 50iterations 0.1033085 3.704736 at 60iterations 4.9080949E-02 1.761444 at 70iterations 2.3319429E-02 0.7007771 at 80iterations 1.1121986E-02 0.3429790 at 90iterations 5.3248596E-03 0.1757948 at 100iterations 2.5433379E-03 7.6690674E-02 at 110iterations 1.2178372E-03 3.6890030E-02 at 120iterations finished qdiffx linear iterations at : 16:05:59 total time elapsed so far: 9.720000 # loops : 120 mean,max change (kT/e) : 1.2178372E-03 3.6890030E-02 energy calculations done at 9.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.910000 DelPhi exited at 16:06:00 9.908u 0.297s 0:10.48 97.2% 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 8 2011 at 16:06:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2332 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.942257 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): -2.409000 45.62100 ymin,ymax (A): -16.93400 29.38100 zmin,zma (A): -17.37000 37.07800 x,y,z range (A): 48.03000 46.31500 54.44800 scale (grids/A): 2.942257 object centre (A): 21.60600 6.223500 9.853999 number of atom coordinates read : 2332 total number of charged atoms : 2273 net assigned charge : 5.000003 assigned positive charge : 347.8110 centred at (gu) : 92.94606 85.24550 90.96439 assigned negative charge : -342.8117 centred at (gu) : 92.88333 85.89568 90.97786 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 168471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20978 grid for indexing accessible points = 1.400000 m= 85505 mr = 121812 m= 32922 mr = 69500 m= 8856 mr = 26678 m= 1432 mr = 6900 m= 117 mr = 1010 m= 1 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 1008 time to turn everything in is 1.550000 number of dielectric boundary points 71341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 18184 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) : 1.961505 object centre at (A) : 21.60600 6.223500 9.853999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2145176 0.2131680 midg,1,midg; midg,igrid,midg 0.2253799 -7.0944741E-02 1,midg,midg; igrid,midg,midg 4.3308701E-02 -0.5434494 gauss-seidel spectral radius is 0.9992740 estimated iterations to convergence 293 setup time was (sec) 1.900000 now iterating at: 16:06:02 rms-change max change #iterations 9.796103 476.1334 at 10iterations 5.766043 123.3347 at 20iterations 3.382025 63.83923 at 30iterations 1.975041 38.89016 at 40iterations 1.156228 23.74360 at 50iterations 0.6740644 12.49950 at 60iterations 0.3912255 7.110634 at 70iterations 0.2274311 4.526500 at 80iterations 0.1323260 2.350260 at 90iterations 7.6628394E-02 1.464891 at 100iterations 4.4426575E-02 0.7992079 at 110iterations 2.5726985E-02 0.5033405 at 120iterations 1.4899995E-02 0.3063660 at 130iterations 8.6158598E-03 0.1572244 at 140iterations 4.9997442E-03 9.2758179E-02 at 150iterations 2.9015609E-03 6.0576439E-02 at 160iterations 1.6880714E-03 3.0555725E-02 at 170iterations 9.8629831E-04 1.7776489E-02 at 180iterations finished qdiffx linear iterations at : 16:06:15 total time elapsed so far: 15.42000 # loops : 180 mean,max change (kT/e) : 9.8629831E-04 1.7776489E-02 energy calculations done at 15.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.61000 DelPhi exited at 16:06:16 15.611u 0.283s 0:16.18 98.2% 0+0k 0+0io 0pf+0w