Wed Dec 21 14:22:42 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+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 Wed Dec 21 2011 at 14:22:42 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1949 !!! WARNING: GLM 8 has a net charge of -0.0940 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6053187 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): 8.765000 49.06500 ymin,ymax (A): -15.46600 26.38300 zmin,zma (A): -11.06400 47.74800 x,y,z range (A): 40.30000 41.84900 58.81200 scale (grids/A): 0.6053187 object centre (A): 28.91500 5.458500 18.34200 number of atom coordinates read : 1949 total number of charged atoms : 1812 net assigned charge : 2.587004 assigned positive charge : 287.4261 centred at (gu) : 91.06571 90.28474 89.77785 assigned negative charge : -284.8393 centred at (gu) : 91.19519 90.41641 89.78560 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4700 nv = 96 ne = 84 npr = 40818 no. pairs analyzed = 40818 no. exposed pairs = 2397 no. arc points = 16986 no. surface atoms = 821 nbur = 1128 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 215 mr = 2507 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1736 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 5757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7073529E-09 1.0848487E-09 midg,1,midg; midg,igrid,midg 5.1262981E-09 -3.0244698E-09 1,midg,midg; igrid,midg,midg 4.2487001E-09 -3.5487575E-09 gauss-seidel spectral radius is 0.9858158 estimated iterations to convergence 69 setup time was (sec) 0.5800000 now iterating at: 14:22:43 rms-change max change #iterations 9.9972218E-02 18.11168 at 10iterations 8.5891364E-03 1.511823 at 20iterations 7.2947080E-04 0.1259093 at 30iterations 6.2395076E-05 1.1581421E-02 at 40iterations 5.5195492E-06 8.8405609E-04 at 50iterations finished qdiffx linear iterations at : 14:22:47 total time elapsed so far: 4.890000 # loops : 50 mean,max change (kT/e) : 5.5195492E-06 8.8405609E-04 energy calculations done at 4.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.080000 DelPhi exited at 14:22:53 5.084u 0.314s 0:11.87 45.4% 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 Wed Dec 21 2011 at 14:22:55 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1949 !!! WARNING: GLM 8 has a net charge of -0.0940 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.815956 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): 8.765000 49.06500 ymin,ymax (A): -15.46600 26.38300 zmin,zma (A): -11.06400 47.74800 x,y,z range (A): 40.30000 41.84900 58.81200 scale (grids/A): 1.815956 object centre (A): 28.91500 5.458500 18.34200 number of atom coordinates read : 1949 total number of charged atoms : 1812 net assigned charge : 2.587004 assigned positive charge : 287.4261 centred at (gu) : 93.19706 90.85413 89.33344 assigned negative charge : -284.8393 centred at (gu) : 93.58566 91.24941 89.35704 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 50654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16986 grid for indexing accessible points = 1.400000 m= 17311 mr = 34302 m= 2239 mr = 12637 m= 92 mr = 1281 m= 0 mr = 36 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 681 time to turn everything in is 0.4800000 number of dielectric boundary points 22040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 14162 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) : 0.6053187 object centre at (A) : 28.91500 5.458500 18.34200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2851685E-02 2.4955835E-02 midg,1,midg; midg,igrid,midg 8.3225612E-03 -6.6950277E-04 1,midg,midg; igrid,midg,midg 5.9533413E-03 -2.2977521E-03 gauss-seidel spectral radius is 0.9984171 estimated iterations to convergence 199 setup time was (sec) 0.8400000 now iterating at: 14:22:57 rms-change max change #iterations 3.278088 166.0767 at 10iterations 1.441991 55.13525 at 20iterations 0.6399662 25.51330 at 30iterations 0.2821673 10.18084 at 40iterations 0.1242309 4.833576 at 50iterations 5.4717291E-02 2.256352 at 60iterations 2.4227550E-02 0.9663124 at 70iterations 1.0730566E-02 0.4485855 at 80iterations 4.7332011E-03 0.1906834 at 90iterations 2.0903700E-03 8.5430205E-02 at 100iterations 9.2202460E-04 3.4740448E-02 at 110iterations 4.0808556E-04 1.7267227E-02 at 120iterations finished qdiffx linear iterations at : 14:23:08 total time elapsed so far: 11.64000 # loops : 120 mean,max change (kT/e) : 4.0808556E-04 1.7267227E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 14:23:11 11.827u 0.363s 0:15.46 78.7% 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 Dec 21 2011 at 14:23:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1949 !!! WARNING: GLM 8 has a net charge of -0.0940 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.723934 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): 8.765000 49.06500 ymin,ymax (A): -15.46600 26.38300 zmin,zma (A): -11.06400 47.74800 x,y,z range (A): 40.30000 41.84900 58.81200 scale (grids/A): 2.723934 object centre (A): 28.91500 5.458500 18.34200 number of atom coordinates read : 1949 total number of charged atoms : 1812 net assigned charge : 2.587004 assigned positive charge : 287.4261 centred at (gu) : 94.79557 91.28133 89.00025 assigned negative charge : -284.8393 centred at (gu) : 95.37854 91.87420 89.03566 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 117191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16986 grid for indexing accessible points = 1.400000 m= 56824 mr = 83106 m= 18978 mr = 46268 m= 3925 mr = 15212 m= 483 mr = 2907 m= 18 mr = 292 m= 0 mr = 9 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2321 time to turn everything in is 1.170000 number of dielectric boundary points 49625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 14491 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) : 1.815956 object centre at (A) : 28.91500 5.458500 18.34200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2913836 0.2372974 midg,1,midg; midg,igrid,midg 6.6066831E-02 4.1389547E-02 1,midg,midg; igrid,midg,midg 4.1464537E-02 1.4333110E-02 gauss-seidel spectral radius is 0.9991787 estimated iterations to convergence 276 setup time was (sec) 1.580000 now iterating at: 14:23:14 rms-change max change #iterations 7.864675 318.6688 at 10iterations 4.419706 113.4609 at 20iterations 2.480906 56.36138 at 30iterations 1.384723 31.61508 at 40iterations 0.7712877 18.22989 at 50iterations 0.4296187 9.464494 at 60iterations 0.2391081 5.527153 at 70iterations 0.1328547 3.036837 at 80iterations 7.4166298E-02 1.488261 at 90iterations 4.1137852E-02 0.9781895 at 100iterations 2.2889573E-02 0.4923983 at 110iterations 1.2749868E-02 0.2983301 at 120iterations 7.0881438E-03 0.1469326 at 130iterations 3.9461218E-03 9.9622726E-02 at 140iterations 2.1972745E-03 4.6044350E-02 at 150iterations 1.2195638E-03 2.5729179E-02 at 160iterations 6.7857769E-04 1.4865711E-02 at 170iterations 3.7767683E-04 8.6154938E-03 at 180iterations finished qdiffx linear iterations at : 14:23:31 total time elapsed so far: 19.13000 # loops : 180 mean,max change (kT/e) : 3.7767683E-04 8.6154938E-03 energy calculations done at 19.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.31000 DelPhi exited at 14:23:32 19.316u 0.392s 0:20.21 97.4% 0+0k 0+0io 0pf+0w