Tue Nov 22 14:10:39 PST 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 Tue Nov 22 2011 at 14:10:40 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.5763128 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): -35.87400 11.48400 ymin,ymax (A): 0.1109999 42.70900 zmin,zma (A): -5.582000 56.19000 x,y,z range (A): 47.35800 42.59800 61.77200 scale (grids/A): 0.5763128 object centre (A): -12.19500 21.41000 25.30400 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.16088 89.59383 91.43349 assigned negative charge : -286.4003 centred at (gu) : 90.05631 89.72931 91.45512 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4380 nv = 96 ne = 84 npr = 40070 no. pairs analyzed = 40070 no. exposed pairs = 2479 no. arc points = 17534 no. surface atoms = 850 nbur = 1120 mkacc time = 8.0000006E-02 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= 196 mr = 2307 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1848 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5485 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0524746E-10 4.1009218E-10 midg,1,midg; midg,igrid,midg 2.4664386E-09 -1.0431546E-09 1,midg,midg; igrid,midg,midg -7.2470002E-10 1.9361617E-09 gauss-seidel spectral radius is 0.9843799 estimated iterations to convergence 66 setup time was (sec) 0.4500000 now iterating at: 14:10:40 rms-change max change #iterations 7.7199847E-02 15.79067 at 10iterations 5.6570633E-03 1.018972 at 20iterations 4.3799548E-04 7.5942993E-02 at 30iterations 3.3497312E-05 6.0024261E-03 at 40iterations 2.6059474E-06 4.3487549E-04 at 50iterations finished qdiffx linear iterations at : 14:10:47 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 2.6059474E-06 4.3487549E-04 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 14:10:48 3.170u 0.168s 0:08.24 40.4% 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 Tue Nov 22 2011 at 14:10:49 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.728939 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): -35.87400 11.48400 ymin,ymax (A): 0.1109999 42.70900 zmin,zma (A): -5.582000 56.19000 x,y,z range (A): 47.35800 42.59800 61.77200 scale (grids/A): 1.728939 object centre (A): -12.19500 21.41000 25.30400 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.48256 88.78131 94.30051 assigned negative charge : -286.4003 centred at (gu) : 90.16918 89.18804 94.36562 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 47157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17534 grid for indexing accessible points = 1.400000 m= 16771 mr = 31725 m= 2258 mr = 12416 m= 77 mr = 1338 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 20772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 14248 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) : 0.5763128 object centre at (A) : -12.19500 21.41000 25.30400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3842631E-02 2.5057327E-02 midg,1,midg; midg,igrid,midg 2.5960854E-03 -6.1566308E-03 1,midg,midg; igrid,midg,midg -1.7566349E-03 1.0764169E-03 gauss-seidel spectral radius is 0.9982681 estimated iterations to convergence 191 setup time was (sec) 0.6000000 now iterating at: 14:10:53 rms-change max change #iterations 2.919440 172.0923 at 10iterations 1.234331 56.21851 at 20iterations 0.5246586 23.13644 at 30iterations 0.2226373 9.918753 at 40iterations 9.4534092E-02 3.655103 at 50iterations 4.0291123E-02 1.678978 at 60iterations 1.7196646E-02 0.8758955 at 70iterations 7.2767097E-03 0.2866480 at 80iterations 3.1051806E-03 0.1267281 at 90iterations 1.3193864E-03 4.8770428E-02 at 100iterations 5.6313653E-04 2.2789955E-02 at 110iterations 2.3930286E-04 9.1247559E-03 at 120iterations finished qdiffx linear iterations at : 14:11:12 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 2.3930286E-04 9.1247559E-03 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 14:11:13 6.891u 0.178s 0:24.65 28.6% 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 Tue Nov 22 2011 at 14:11:17 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 # of charge parameter records: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.593408 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): -35.87400 11.48400 ymin,ymax (A): 0.1109999 42.70900 zmin,zma (A): -5.582000 56.19000 x,y,z range (A): 47.35800 42.59800 61.77200 scale (grids/A): 2.593408 object centre (A): -12.19500 21.41000 25.30400 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.72381 88.17210 96.45075 assigned negative charge : -286.4003 centred at (gu) : 90.25375 88.78208 96.54848 start vw surface at 0.1100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 109032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17534 grid for indexing accessible points = 1.400000 m= 54388 mr = 76994 m= 18898 mr = 44377 m= 3861 mr = 15399 m= 348 mr = 2789 m= 11 mr = 185 m= 0 mr = 4 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 46790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 14703 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) : 1.728939 object centre at (A) : -12.19500 21.41000 25.30400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1014739 0.2575331 midg,1,midg; midg,igrid,midg -5.4393103E-04 -8.3344653E-02 1,midg,midg; igrid,midg,midg -4.0609375E-02 -1.4325064E-02 gauss-seidel spectral radius is 0.9991326 estimated iterations to convergence 268 setup time was (sec) 1.150000 now iterating at: 14:11:20 rms-change max change #iterations 7.216782 268.6649 at 10iterations 3.983886 116.1498 at 20iterations 2.187986 56.70136 at 30iterations 1.195281 27.94494 at 40iterations 0.6577929 18.18214 at 50iterations 0.3598385 8.958958 at 60iterations 0.1968403 4.308912 at 70iterations 0.1079820 2.765411 at 80iterations 5.8967907E-02 1.526882 at 90iterations 3.2315265E-02 0.7286625 at 100iterations 1.7689742E-02 0.4369965 at 110iterations 9.6568139E-03 0.2406940 at 120iterations 5.2877693E-03 0.1264572 at 130iterations 2.8994677E-03 6.1657906E-02 at 140iterations 1.5840164E-03 3.8704872E-02 at 150iterations 8.6404191E-04 1.9142151E-02 at 160iterations 4.7376103E-04 1.1207819E-02 at 170iterations 2.5878157E-04 6.1302185E-03 at 180iterations finished qdiffx linear iterations at : 14:11:39 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 2.5878157E-04 6.1302185E-03 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 14:11:40 11.791u 0.229s 0:22.74 52.8% 0+0k 0+0io 0pf+0w