Sun Oct 9 14:05:38 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 Sun Oct 9 2011 at 14:05:39 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 = 2387 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6867151 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): 21.44000 70.61600 ymin,ymax (A): -1.765000 50.07600 zmin,zma (A): -5.665000 37.15800 x,y,z range (A): 49.17599 51.84100 42.82300 scale (grids/A): 0.6867151 object centre (A): 46.02800 24.15550 15.74650 number of atom coordinates read : 2387 total number of charged atoms : 2245 net assigned charge : 3.500023 assigned positive charge : 364.2110 centred at (gu) : 90.39455 89.00398 89.08469 assigned negative charge : -360.7115 centred at (gu) : 90.42587 88.84769 89.00679 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7587 nv = 96 ne = 84 npr = 48055 no. pairs analyzed = 48055 no. exposed pairs = 2849 no. arc points = 20650 no. surface atoms = 961 nbur = 1426 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4258 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3000000 number of dielectric boundary points 3720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1939 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8691 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1112647E-08 3.8492495E-08 midg,1,midg; midg,igrid,midg -4.6270397E-08 6.0018124E-08 1,midg,midg; igrid,midg,midg 2.7636402E-08 8.2436395E-09 gauss-seidel spectral radius is 0.9889846 estimated iterations to convergence 78 setup time was (sec) 0.5300000 now iterating at: 14:05:39 rms-change max change #iterations 0.1866308 28.00496 at 10iterations 2.1759385E-02 3.831909 at 20iterations 2.7216875E-03 0.3740234 at 30iterations 4.4795746E-04 8.1269264E-02 at 40iterations 1.1246509E-04 1.8604279E-02 at 50iterations finished qdiffx linear iterations at : 14:05:42 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.1246509E-04 1.8604279E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:05:42 3.379u 0.156s 0:03.89 90.4% 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 Sun Oct 9 2011 at 14:05:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2387 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: 2.060145 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): 21.44000 70.61600 ymin,ymax (A): -1.765000 50.07600 zmin,zma (A): -5.665000 37.15800 x,y,z range (A): 49.17599 51.84100 42.82300 scale (grids/A): 2.060145 object centre (A): 46.02800 24.15550 15.74650 number of atom coordinates read : 2387 total number of charged atoms : 2245 net assigned charge : 3.500023 assigned positive charge : 364.2110 centred at (gu) : 91.18291 87.01137 87.25391 assigned negative charge : -360.7115 centred at (gu) : 91.27741 86.54279 87.02006 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 30626 mr = 56631 m= 5383 mr = 23017 m= 472 mr = 3398 m= 10 mr = 209 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1495 time to turn everything in is 0.6300000 number of dielectric boundary points 34274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17804 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) : 0.6867151 object centre at (A) : 46.02800 24.15550 15.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1719976E-03 4.2464584E-02 midg,1,midg; midg,igrid,midg -4.2212665E-02 1.3703167E-02 1,midg,midg; igrid,midg,midg 3.5191122E-02 -1.4457286E-02 gauss-seidel spectral radius is 0.9988050 estimated iterations to convergence 229 setup time was (sec) 0.9200000 now iterating at: 14:05:44 rms-change max change #iterations 4.723382 213.2054 at 10iterations 2.316109 80.09178 at 20iterations 1.135929 32.73964 at 30iterations 0.5608147 17.52975 at 40iterations 0.2762255 9.387941 at 50iterations 0.1357873 4.114867 at 60iterations 6.6939965E-02 2.038573 at 70iterations 3.3078905E-02 0.9462154 at 80iterations 1.6203579E-02 0.4713879 at 90iterations 8.0626821E-03 0.2483177 at 100iterations 3.9940351E-03 0.1166573 at 110iterations 1.9987095E-03 6.0549736E-02 at 120iterations finished qdiffx linear iterations at : 14:05:50 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 1.9987095E-03 6.0549736E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 14:05:51 7.641u 0.171s 0:08.07 96.7% 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 Sun Oct 9 2011 at 14:05:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2387 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.090218 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): 21.44000 70.61600 ymin,ymax (A): -1.765000 50.07600 zmin,zma (A): -5.665000 37.15800 x,y,z range (A): 49.17599 51.84100 42.82300 scale (grids/A): 3.090218 object centre (A): 46.02800 24.15550 15.74650 number of atom coordinates read : 2387 total number of charged atoms : 2245 net assigned charge : 3.500023 assigned positive charge : 364.2110 centred at (gu) : 91.77425 85.51684 85.88072 assigned negative charge : -360.7115 centred at (gu) : 91.91605 84.81416 85.53006 start vw surface at 0.1600000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 187006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 97382 mr = 136846 m= 37147 mr = 80463 m= 9858 mr = 30162 m= 1825 mr = 7373 m= 207 mr = 1244 m= 8 mr = 140 m= 0 mr = 4 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 5310 time to turn everything in is 1.920000 number of dielectric boundary points 77201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 17960 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) : 2.060145 object centre at (A) : 46.02800 24.15550 15.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8548911E-02 0.3814656 midg,1,midg; midg,igrid,midg -0.4367185 0.3492698 1,midg,midg; igrid,midg,midg 0.3738427 -0.4081737 gauss-seidel spectral radius is 0.9992911 estimated iterations to convergence 296 setup time was (sec) 2.230000 now iterating at: 14:05:53 rms-change max change #iterations 10.69058 419.9886 at 10iterations 6.293890 129.9307 at 20iterations 3.704564 68.05303 at 30iterations 2.176680 46.65991 at 40iterations 1.277275 25.00889 at 50iterations 0.7477808 12.42246 at 60iterations 0.4374693 7.997940 at 70iterations 0.2556230 4.521018 at 80iterations 0.1491236 2.580498 at 90iterations 8.7186545E-02 1.519348 at 100iterations 5.0740208E-02 0.8914146 at 110iterations 2.9636605E-02 0.4982414 at 120iterations 1.7303066E-02 0.3023615 at 130iterations 1.0134510E-02 0.1685677 at 140iterations 5.9403158E-03 0.1004715 at 150iterations 3.5172205E-03 6.6251755E-02 at 160iterations 2.1016875E-03 3.7147522E-02 at 170iterations 1.2828367E-03 2.3638725E-02 at 180iterations finished qdiffx linear iterations at : 14:06:04 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 1.2828367E-03 2.3638725E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 14:06:04 12.992u 0.177s 0:13.44 97.9% 0+0k 0+0io 0pf+0w