Tue Oct 11 03:20:45 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 Tue Oct 11 2011 at 03:20:45 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 = 3214 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5364031 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): -20.47200 38.71600 ymin,ymax (A): 24.22600 75.26600 zmin,zma (A): 70.96900 137.3370 x,y,z range (A): 59.18800 51.04000 66.36800 scale (grids/A): 0.5364031 object centre (A): 9.122002 49.74600 104.1530 number of atom coordinates read : 3214 total number of charged atoms : 3075 net assigned charge : -6.999980 assigned positive charge : 481.4187 centred at (gu) : 88.25568 88.64963 92.67873 assigned negative charge : -488.4198 centred at (gu) : 88.25333 88.69677 92.73689 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5809 nv = 96 ne = 84 npr = 66806 no. pairs analyzed = 66806 no. exposed pairs = 3905 no. arc points = 27480 no. surface atoms = 1317 nbur = 1897 mkacc time = 0.1100000 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 = 1.596000 m= 229 mr = 3019 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2867 ## 418 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3959259E-12 -1.1449385E-09 midg,1,midg; midg,igrid,midg -6.9602012E-11 -3.7532397E-10 1,midg,midg; igrid,midg,midg -4.6025822E-10 -1.8118694E-10 gauss-seidel spectral radius is 0.9821010 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 03:20:45 rms-change max change #iterations 6.9967292E-02 11.23507 at 10iterations 4.5522959E-03 0.7209892 at 20iterations 3.3083526E-04 6.2833786E-02 at 30iterations 4.2117950E-05 8.1702173E-03 at 40iterations 8.1991257E-06 1.7248690E-03 at 50iterations finished qdiffx linear iterations at : 03:20:48 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 8.1991257E-06 1.7248690E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 03:20:49 3.471u 0.173s 0:04.10 88.7% 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 Tue Oct 11 2011 at 03:20:49 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 = 3214 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: 1.609209 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): -20.47200 38.71600 ymin,ymax (A): 24.22600 75.26600 zmin,zma (A): 70.96900 137.3370 x,y,z range (A): 59.18800 51.04000 66.36800 scale (grids/A): 1.609209 object centre (A): 9.122002 49.74600 104.1530 number of atom coordinates read : 3214 total number of charged atoms : 3075 net assigned charge : -6.999980 assigned positive charge : 481.4187 centred at (gu) : 84.76594 85.94810 98.03513 assigned negative charge : -488.4198 centred at (gu) : 84.75954 86.08994 98.21024 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64783 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19902 mr = 44026 m= 1992 mr = 13845 m= 53 mr = 1035 m= 0 mr = 6 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 171 time to turn everything in is 0.3300000 number of dielectric boundary points 27818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 369 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 23420 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) : 0.5364031 object centre at (A) : 9.122002 49.74600 104.1530 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3872312E-02 -1.4652414E-02 midg,1,midg; midg,igrid,midg -3.7760078E-03 -5.9502237E-03 1,midg,midg; igrid,midg,midg 2.0724919E-03 -3.9657569E-03 gauss-seidel spectral radius is 0.9981388 estimated iterations to convergence 184 setup time was (sec) 0.5600000 now iterating at: 03:20:50 rms-change max change #iterations 3.324212 159.5863 at 10iterations 1.374675 55.39580 at 20iterations 0.5672501 20.71124 at 30iterations 0.2339892 8.492248 at 40iterations 9.6672483E-02 4.408412 at 50iterations 3.9789122E-02 1.315339 at 60iterations 1.6447917E-02 0.6645813 at 70iterations 6.8155034E-03 0.2396669 at 80iterations 2.8168296E-03 0.1033325 at 90iterations 1.1730677E-03 4.2294264E-02 at 100iterations 4.9279560E-04 1.7152786E-02 at 110iterations 2.0792737E-04 7.4958801E-03 at 120iterations finished qdiffx linear iterations at : 03:20:57 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.0792737E-04 7.4958801E-03 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 03:20:57 7.855u 0.197s 0:08.63 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 Tue Oct 11 2011 at 03:20:57 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 = 3214 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: 2.413814 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): -20.47200 38.71600 ymin,ymax (A): 24.22600 75.26600 zmin,zma (A): 70.96900 137.3370 x,y,z range (A): 59.18800 51.04000 66.36800 scale (grids/A): 2.413814 object centre (A): 9.122002 49.74600 104.1530 number of atom coordinates read : 3214 total number of charged atoms : 3075 net assigned charge : -6.999980 assigned positive charge : 481.4187 centred at (gu) : 82.14865 83.92179 102.0525 assigned negative charge : -488.4198 centred at (gu) : 82.13933 84.13479 102.3152 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 150478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 69191 mr = 107664 m= 19641 mr = 55095 m= 3202 mr = 14827 m= 194 mr = 2167 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 487 time to turn everything in is 0.8000000 number of dielectric boundary points 62885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24554 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) : 1.609209 object centre at (A) : 9.122002 49.74600 104.1530 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4156371 -0.3292614 midg,1,midg; midg,igrid,midg -4.2330887E-02 -9.0104274E-02 1,midg,midg; igrid,midg,midg 0.1362789 -2.2165896E-03 gauss-seidel spectral radius is 0.9991244 estimated iterations to convergence 267 setup time was (sec) 1.030000 now iterating at: 03:20:59 rms-change max change #iterations 8.774850 289.1901 at 10iterations 4.895338 111.7648 at 20iterations 2.716051 62.11104 at 30iterations 1.502329 35.92631 at 40iterations 0.8275700 18.46128 at 50iterations 0.4538106 10.43089 at 60iterations 0.2495551 5.068288 at 70iterations 0.1370083 3.071827 at 80iterations 7.4912138E-02 1.546156 at 90iterations 4.1161314E-02 0.8667297 at 100iterations 2.2521190E-02 0.5026979 at 110iterations 1.2338452E-02 0.2453880 at 120iterations 6.7503634E-03 0.1384108 at 130iterations 3.7103798E-03 7.8689575E-02 at 140iterations 2.0308965E-03 4.0122986E-02 at 150iterations 1.1166299E-03 2.3164749E-02 at 160iterations 6.1724422E-04 1.2650013E-02 at 170iterations 3.4228293E-04 7.3337555E-03 at 180iterations finished qdiffx linear iterations at : 03:21:10 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 3.4228293E-04 7.3337555E-03 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 03:21:11 12.515u 0.229s 0:13.28 95.8% 0+0k 0+0io 0pf+0w