Wed Dec 21 14:20:51 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 Wed Dec 21 2011 at 14:20:51 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5992761 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): -24.42500 34.98000 ymin,ymax (A): -19.65300 20.73300 zmin,zma (A): -2.867000 38.74400 x,y,z range (A): 59.40500 40.38600 41.61100 scale (grids/A): 0.5992761 object centre (A): 5.277502 0.5400000 17.93850 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 263.8745 centred at (gu) : 89.77971 90.38490 90.28987 assigned negative charge : -285.8263 centred at (gu) : 89.77618 90.48961 90.43664 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4810 nv = 96 ne = 84 npr = 39689 no. pairs analyzed = 39689 no. exposed pairs = 2394 no. arc points = 17086 no. surface atoms = 808 nbur = 1156 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 203 mr = 2647 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.1700000 number of dielectric boundary points 2359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1632 ## 133 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 5700 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0467808E-09 -1.3958733E-08 midg,1,midg; midg,igrid,midg -5.9292589E-09 -1.3014655E-08 1,midg,midg; igrid,midg,midg -9.7108108E-09 -8.6378140E-09 gauss-seidel spectral radius is 0.9855374 estimated iterations to convergence 68 setup time was (sec) 0.4000000 now iterating at: 14:20:51 rms-change max change #iterations 9.4634093E-02 16.93567 at 10iterations 8.0661615E-03 1.381166 at 20iterations 6.6898344E-04 0.1195145 at 30iterations 5.7986916E-05 1.0910034E-02 at 40iterations 4.8004717E-06 9.9563599E-04 at 50iterations finished qdiffx linear iterations at : 14:20:55 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 4.8004717E-06 9.9563599E-04 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 14:20:56 4.263u 0.334s 0:04.92 93.2% 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 Wed Dec 21 2011 at 14:20:56 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.797828 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): -24.42500 34.98000 ymin,ymax (A): -19.65300 20.73300 zmin,zma (A): -2.867000 38.74400 x,y,z range (A): 59.40500 40.38600 41.61100 scale (grids/A): 1.797828 object centre (A): 5.277502 0.5400000 17.93850 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 263.8745 centred at (gu) : 89.33931 91.15478 90.87011 assigned negative charge : -285.8263 centred at (gu) : 89.32841 91.46905 91.31009 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 52524 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17086 grid for indexing accessible points = 1.400000 m= 18693 mr = 36236 m= 2318 mr = 14242 m= 67 mr = 1438 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.2800000 number of dielectric boundary points 21672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 13799 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) : 0.5992761 object centre at (A) : 5.277502 0.5400000 17.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4534095E-03 -3.2313667E-02 midg,1,midg; midg,igrid,midg -1.4279766E-02 -2.9574171E-02 1,midg,midg; igrid,midg,midg -2.0610373E-02 -2.5559317E-02 gauss-seidel spectral radius is 0.9983946 estimated iterations to convergence 198 setup time was (sec) 0.6000000 now iterating at: 14:20:57 rms-change max change #iterations 3.155390 143.8402 at 10iterations 1.385225 54.54459 at 20iterations 0.6081029 22.00989 at 30iterations 0.2667602 11.27818 at 40iterations 0.1167244 4.566185 at 50iterations 5.1444061E-02 1.975401 at 60iterations 2.2538735E-02 0.8629417 at 70iterations 9.8595973E-03 0.4079247 at 80iterations 4.3472801E-03 0.1676521 at 90iterations 1.9043873E-03 7.1927547E-02 at 100iterations 8.3736825E-04 3.0654907E-02 at 110iterations 3.6847449E-04 1.5186310E-02 at 120iterations finished qdiffx linear iterations at : 14:21:06 total time elapsed so far: 9.960000 # loops : 120 mean,max change (kT/e) : 3.6847449E-04 1.5186310E-02 energy calculations done at 9.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.09000 DelPhi exited at 14:21:07 10.091u 0.363s 0:11.02 94.8% 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 14:21:07 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.696743 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): -24.42500 34.98000 ymin,ymax (A): -19.65300 20.73300 zmin,zma (A): -2.867000 38.74400 x,y,z range (A): 59.40500 40.38600 41.61100 scale (grids/A): 2.696743 object centre (A): 5.277502 0.5400000 17.93850 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 263.8745 centred at (gu) : 89.00911 91.73219 91.30529 assigned negative charge : -285.8263 centred at (gu) : 88.99270 92.20365 91.96524 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 121346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17086 grid for indexing accessible points = 1.400000 m= 61601 mr = 87601 m= 20722 mr = 51261 m= 3928 mr = 16976 m= 296 mr = 2963 m= 5 mr = 173 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2093 time to turn everything in is 0.7100000 number of dielectric boundary points 48924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 14112 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) : 1.797828 object centre at (A) : 5.277502 0.5400000 17.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7485332E-02 -0.3475674 midg,1,midg; midg,igrid,midg -0.1536846 -0.3318015 1,midg,midg; igrid,midg,midg -0.1856989 -0.3188005 gauss-seidel spectral radius is 0.9991726 estimated iterations to convergence 275 setup time was (sec) 1.040000 now iterating at: 14:21:08 rms-change max change #iterations 7.611654 273.3785 at 10iterations 4.308061 126.4870 at 20iterations 2.411981 65.90443 at 30iterations 1.343534 33.70486 at 40iterations 0.7477143 18.71459 at 50iterations 0.4169577 11.01002 at 60iterations 0.2323273 5.406568 at 70iterations 0.1287881 2.802446 at 80iterations 7.1338288E-02 1.594814 at 90iterations 3.9672945E-02 0.8561401 at 100iterations 2.2026176E-02 0.4706259 at 110iterations 1.2241585E-02 0.2622585 at 120iterations 6.7918277E-03 0.1530819 at 130iterations 3.7732730E-03 8.1408501E-02 at 140iterations 2.0868655E-03 4.5072556E-02 at 150iterations 1.1608732E-03 2.4993896E-02 at 160iterations 6.4347626E-04 1.4206886E-02 at 170iterations 3.5838137E-04 8.1467628E-03 at 180iterations finished qdiffx linear iterations at : 14:21:21 total time elapsed so far: 13.92000 # loops : 180 mean,max change (kT/e) : 3.5838137E-04 8.1467628E-03 energy calculations done at 13.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.05000 DelPhi exited at 14:21:30 14.047u 0.352s 0:24.92 57.7% 0+0k 0+0io 0pf+0w