Tue Oct 11 03:26:02 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 03:26:02 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 = 2662 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: 0.5644253 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): -13.37400 36.99800 ymin,ymax (A): -25.68600 37.38700 zmin,zma (A): -14.99300 34.84800 x,y,z range (A): 50.37200 63.07300 49.84100 scale (grids/A): 0.5644253 object centre (A): 11.81200 5.850499 9.927502 number of atom coordinates read : 2662 total number of charged atoms : 2517 net assigned charge : 9.000027 assigned positive charge : 403.7309 centred at (gu) : 88.23167 88.72324 90.31112 assigned negative charge : -394.7317 centred at (gu) : 88.14661 88.79777 90.29831 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5567 nv = 96 ne = 84 npr = 53483 no. pairs analyzed = 53483 no. exposed pairs = 3342 no. arc points = 23992 no. surface atoms = 1121 nbur = 1541 mkacc time = 9.0000004E-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= 215 mr = 2891 m= 0 mr = 9 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2480 ## 319 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1380981E-10 1.3711164E-09 midg,1,midg; midg,igrid,midg 2.6784899E-09 2.0940460E-10 1,midg,midg; igrid,midg,midg 1.8854783E-10 1.3789337E-09 gauss-seidel spectral radius is 0.9837819 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 03:26:03 rms-change max change #iterations 7.9193957E-02 14.20854 at 10iterations 5.7893274E-03 0.8576479 at 20iterations 5.9061253E-04 0.1066074 at 30iterations 1.5180439E-04 3.4045219E-02 at 40iterations 5.3130887E-05 1.2146950E-02 at 50iterations finished qdiffx linear iterations at : 03:26:05 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 5.3130887E-05 1.2146950E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 03:26:06 3.391u 0.181s 0:03.99 89.4% 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 Oct 11 2011 at 03:26:06 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 = 2662 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: 1.693276 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): -13.37400 36.99800 ymin,ymax (A): -25.68600 37.38700 zmin,zma (A): -14.99300 34.84800 x,y,z range (A): 50.37200 63.07300 49.84100 scale (grids/A): 1.693276 object centre (A): 11.81200 5.850499 9.927502 number of atom coordinates read : 2662 total number of charged atoms : 2517 net assigned charge : 9.000027 assigned positive charge : 403.7309 centred at (gu) : 84.69462 86.16907 90.93287 assigned negative charge : -394.7317 centred at (gu) : 84.43964 86.39319 90.89471 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 61331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23992 grid for indexing accessible points = 1.400000 m= 19164 mr = 41474 m= 2135 mr = 13341 m= 50 mr = 1128 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.3100000 number of dielectric boundary points 26734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19412 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) : 0.5644253 object centre at (A) : 11.81200 5.850499 9.927502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2995314E-03 1.2639183E-02 midg,1,midg; midg,igrid,midg 2.1003485E-02 -8.3795758E-03 1,midg,midg; igrid,midg,midg 3.0237082E-03 1.7511678E-03 gauss-seidel spectral radius is 0.9982811 estimated iterations to convergence 192 setup time was (sec) 0.5400000 now iterating at: 03:26:07 rms-change max change #iterations 3.360626 170.0165 at 10iterations 1.422425 60.54785 at 20iterations 0.6064346 25.59641 at 30iterations 0.2587696 10.76682 at 40iterations 0.1104513 4.337463 at 50iterations 4.7109760E-02 1.898472 at 60iterations 2.0167077E-02 0.8921242 at 70iterations 8.6150886E-03 0.3067212 at 80iterations 3.6992361E-03 0.1312828 at 90iterations 1.6168063E-03 5.5781603E-02 at 100iterations 7.2556123E-04 2.7204514E-02 at 110iterations 3.4606812E-04 1.5605927E-02 at 120iterations finished qdiffx linear iterations at : 03:26:14 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 3.4606812E-04 1.5605927E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 03:26:14 7.679u 0.186s 0:08.40 93.4% 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 Oct 11 2011 at 03:26:15 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 = 2662 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: 2.539914 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): -13.37400 36.99800 ymin,ymax (A): -25.68600 37.38700 zmin,zma (A): -14.99300 34.84800 x,y,z range (A): 50.37200 63.07300 49.84100 scale (grids/A): 2.539914 object centre (A): 11.81200 5.850499 9.927502 number of atom coordinates read : 2662 total number of charged atoms : 2517 net assigned charge : 9.000027 assigned positive charge : 403.7309 centred at (gu) : 82.04183 84.25352 91.39928 assigned negative charge : -394.7317 centred at (gu) : 81.65939 84.58957 91.34204 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 142295 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23992 grid for indexing accessible points = 1.400000 m= 65563 mr = 101096 m= 19333 mr = 52047 m= 3453 mr = 14931 m= 265 mr = 2380 m= 1 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 251 time to turn everything in is 0.7300000 number of dielectric boundary points 60322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20119 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) : 1.693276 object centre at (A) : 11.81200 5.850499 9.927502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5737933E-02 0.2366248 midg,1,midg; midg,igrid,midg 0.2130245 -0.1649226 1,midg,midg; igrid,midg,midg 4.3117080E-02 -2.8271232E-02 gauss-seidel spectral radius is 0.9991601 estimated iterations to convergence 273 setup time was (sec) 0.9600000 now iterating at: 03:26:16 rms-change max change #iterations 8.454639 359.9277 at 10iterations 4.747206 133.0172 at 20iterations 2.651859 56.12272 at 30iterations 1.485130 33.36447 at 40iterations 0.8255802 17.58723 at 50iterations 0.4601669 10.27307 at 60iterations 0.2559408 5.669144 at 70iterations 0.1422985 3.335192 at 80iterations 7.8818686E-02 1.734686 at 90iterations 4.3717735E-02 0.9859009 at 100iterations 2.4234496E-02 0.5266666 at 110iterations 1.3451696E-02 0.2750244 at 120iterations 7.4543403E-03 0.1543598 at 130iterations 4.1383873E-03 8.6763382E-02 at 140iterations 2.3115682E-03 4.6958923E-02 at 150iterations 1.2931682E-03 2.9194832E-02 at 160iterations 7.2931824E-04 1.7830849E-02 at 170iterations 4.1975224E-04 9.3493462E-03 at 180iterations finished qdiffx linear iterations at : 03:26:27 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 4.1975224E-04 9.3493462E-03 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 03:26:27 12.043u 0.205s 0:12.57 97.3% 0+0k 0+0io 0pf+0w