Sat Oct 8 17:38:08 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 17:38:08 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 = 3509 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5243853 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): -0.7969999 44.38900 ymin,ymax (A): -30.54600 25.53100 zmin,zma (A): 1.187000 69.07600 x,y,z range (A): 45.18600 56.07700 67.88901 scale (grids/A): 0.5243853 object centre (A): 21.79600 -2.507500 35.13150 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : -5.771982 assigned positive charge : 532.0942 centred at (gu) : 90.41086 92.07746 90.60947 assigned negative charge : -537.8677 centred at (gu) : 90.36259 92.02880 90.60296 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6058 nv = 96 ne = 84 npr = 71374 no. pairs analyzed = 71374 no. exposed pairs = 4248 no. arc points = 28950 no. surface atoms = 1446 nbur = 2063 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 = 1.624000 m= 238 mr = 3233 m= 1 mr = 11 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 0.4400000 number of dielectric boundary points 3053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2946 ## 427 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8158 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5071600E-10 -1.5201400E-10 midg,1,midg; midg,igrid,midg -1.9046593E-10 2.9977302E-11 1,midg,midg; igrid,midg,midg -2.8867186E-10 1.4514356E-11 gauss-seidel spectral radius is 0.9812993 estimated iterations to convergence 60 setup time was (sec) 0.7100000 now iterating at: 17:38:09 rms-change max change #iterations 6.4794496E-02 10.59655 at 10iterations 3.9189407E-03 0.6466160 at 20iterations 2.8971021E-04 4.4901848E-02 at 30iterations 3.5655572E-05 5.5789948E-03 at 40iterations 6.6115172E-06 1.0185242E-03 at 50iterations finished qdiffx linear iterations at : 17:38:13 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 6.6115172E-06 1.0185242E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 17:38:13 4.250u 0.277s 0:04.80 94.1% 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 17:38:13 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3509 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.573156 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): -0.7969999 44.38900 ymin,ymax (A): -30.54600 25.53100 zmin,zma (A): 1.187000 69.07600 x,y,z range (A): 45.18600 56.07700 67.88901 scale (grids/A): 1.573156 object centre (A): 21.79600 -2.507500 35.13150 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : -5.771982 assigned positive charge : 532.0942 centred at (gu) : 91.23156 96.23136 91.82758 assigned negative charge : -537.8677 centred at (gu) : 91.08742 96.08587 91.80865 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 68764 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28950 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20630 mr = 47926 m= 1850 mr = 14169 m= 31 mr = 794 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 115 time to turn everything in is 0.6200000 number of dielectric boundary points 28386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 454 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 25487 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) : 0.5243853 object centre at (A) : 21.79600 -2.507500 35.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4121820E-03 9.1991685E-03 midg,1,midg; midg,igrid,midg -7.9604685E-03 -1.2151431E-02 1,midg,midg; igrid,midg,midg -5.0938651E-03 1.0762255E-03 gauss-seidel spectral radius is 0.9980766 estimated iterations to convergence 181 setup time was (sec) 0.9200000 now iterating at: 17:38:14 rms-change max change #iterations 3.348352 150.7040 at 10iterations 1.363616 57.95090 at 20iterations 0.5518732 18.65707 at 30iterations 0.2254869 8.087196 at 40iterations 9.1695227E-02 3.293194 at 50iterations 3.7438706E-02 1.409776 at 60iterations 1.5207168E-02 0.5258541 at 70iterations 6.2428229E-03 0.2446295 at 80iterations 2.5708708E-03 9.2211723E-02 at 90iterations 1.0721950E-03 3.9741039E-02 at 100iterations 4.6192177E-04 1.8007278E-02 at 110iterations 2.1065312E-04 7.2803497E-03 at 120iterations finished qdiffx linear iterations at : 17:38:23 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 2.1065312E-04 7.2803497E-03 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 17:38:23 9.571u 0.338s 0:10.16 97.4% 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 Sat Oct 8 2011 at 17:38:23 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 = 3509 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.359734 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): -0.7969999 44.38900 ymin,ymax (A): -30.54600 25.53100 zmin,zma (A): 1.187000 69.07600 x,y,z range (A): 45.18600 56.07700 67.88901 scale (grids/A): 2.359734 object centre (A): 21.79600 -2.507500 35.13150 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : -5.771982 assigned positive charge : 532.0942 centred at (gu) : 91.84714 99.34672 92.74107 assigned negative charge : -537.8677 centred at (gu) : 91.63101 99.12859 92.71290 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 159935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28950 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73151 mr = 117119 m= 19165 mr = 58075 m= 2708 mr = 14159 m= 118 mr = 1634 m= 0 mr = 25 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 365 time to turn everything in is 1.480000 number of dielectric boundary points 64065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 26843 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) : 1.573156 object centre at (A) : 21.79600 -2.507500 35.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1834751 6.8522193E-02 midg,1,midg; midg,igrid,midg -0.1153074 -0.1779721 1,midg,midg; igrid,midg,midg -8.7373286E-02 4.4000350E-02 gauss-seidel spectral radius is 0.9991070 estimated iterations to convergence 264 setup time was (sec) 1.820000 now iterating at: 17:38:25 rms-change max change #iterations 8.880759 252.9449 at 10iterations 4.926711 132.8320 at 20iterations 2.719875 62.85938 at 30iterations 1.497223 41.69499 at 40iterations 0.8205867 17.53663 at 50iterations 0.4476257 9.255033 at 60iterations 0.2450639 4.872314 at 70iterations 0.1333955 2.958836 at 80iterations 7.2883144E-02 1.366695 at 90iterations 3.9579805E-02 0.8388062 at 100iterations 2.1545419E-02 0.4835041 at 110iterations 1.1728568E-02 0.2404480 at 120iterations 6.3918033E-03 0.1367149 at 130iterations 3.4832938E-03 7.5180054E-02 at 140iterations 1.9008614E-03 3.7799835E-02 at 150iterations 1.0393148E-03 2.0640373E-02 at 160iterations 5.7159353E-04 1.1713028E-02 at 170iterations 3.1803994E-04 6.9007874E-03 at 180iterations finished qdiffx linear iterations at : 17:38:39 total time elapsed so far: 15.78000 # loops : 180 mean,max change (kT/e) : 3.1803994E-04 6.9007874E-03 energy calculations done at 15.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.96000 DelPhi exited at 17:38:40 15.960u 0.353s 0:16.60 98.2% 0+0k 0+0io 0pf+0w