Sat Oct 15 13:54:55 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+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 Sat Oct 15 2011 at 13:54:55 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 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: 0.5609391 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): -7.488000 39.44600 ymin,ymax (A): -9.726000 42.76600 zmin,zma (A): -1.126000 62.33900 x,y,z range (A): 46.93400 52.49200 63.46500 scale (grids/A): 0.5609391 object centre (A): 15.97900 16.52000 30.60650 number of atom coordinates read : 2785 total number of charged atoms : 2644 net assigned charge : 3.000026 assigned positive charge : 413.7626 centred at (gu) : 90.35140 89.47149 89.38424 assigned negative charge : -410.7635 centred at (gu) : 90.30309 89.39912 89.43359 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5783 nv = 96 ne = 84 npr = 55149 no. pairs analyzed = 55149 no. exposed pairs = 3818 no. arc points = 26890 no. surface atoms = 1275 nbur = 1510 mkacc time = 0.1000000 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 = 1.540000 m= 257 mr = 2824 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2754 ## 345 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7498 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8535946E-10 -1.6627200E-10 midg,1,midg; midg,igrid,midg -5.0715393E-10 9.5851815E-10 1,midg,midg; igrid,midg,midg -1.6811595E-10 9.1233660E-10 gauss-seidel spectral radius is 0.9835973 estimated iterations to convergence 64 setup time was (sec) 0.4200000 now iterating at: 13:54:55 rms-change max change #iterations 7.9196058E-02 14.05352 at 10iterations 5.5484027E-03 0.8637164 at 20iterations 4.2832547E-04 6.6071510E-02 at 30iterations 4.3046737E-05 6.9828033E-03 at 40iterations 6.2657332E-06 1.0070801E-03 at 50iterations finished qdiffx linear iterations at : 13:54:58 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 6.2657332E-06 1.0070801E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 13:54:59 3.619u 0.191s 0:04.10 92.6% 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 Sat Oct 15 2011 at 13:54:59 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 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: 1.682817 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): -7.488000 39.44600 ymin,ymax (A): -9.726000 42.76600 zmin,zma (A): -1.126000 62.33900 x,y,z range (A): 46.93400 52.49200 63.46500 scale (grids/A): 1.682817 object centre (A): 15.97900 16.52000 30.60650 number of atom coordinates read : 2785 total number of charged atoms : 2644 net assigned charge : 3.000026 assigned positive charge : 413.7626 centred at (gu) : 91.05374 88.41399 88.15202 assigned negative charge : -410.7635 centred at (gu) : 90.90908 88.19712 88.30045 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63997 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26890 grid for indexing accessible points = 1.400000 m= 19536 mr = 42050 m= 2140 mr = 12934 m= 57 mr = 956 m= 0 mr = 6 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 29784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20385 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) : 0.5609391 object centre at (A) : 15.97900 16.52000 30.60650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6553081E-02 1.3795624E-02 midg,1,midg; midg,igrid,midg -1.3885655E-02 -2.6671258E-03 1,midg,midg; igrid,midg,midg 5.7350122E-04 2.3836233E-03 gauss-seidel spectral radius is 0.9982880 estimated iterations to convergence 192 setup time was (sec) 0.5500000 now iterating at: 13:55:00 rms-change max change #iterations 3.380576 156.5100 at 10iterations 1.435739 52.83435 at 20iterations 0.6124367 22.32681 at 30iterations 0.2603818 9.506691 at 40iterations 0.1117393 3.808419 at 50iterations 4.7581267E-02 1.828297 at 60iterations 2.0224098E-02 0.7619400 at 70iterations 8.6658550E-03 0.3373947 at 80iterations 3.6961779E-03 0.1371698 at 90iterations 1.5830385E-03 5.3539276E-02 at 100iterations 6.7655277E-04 2.2708893E-02 at 110iterations 2.8963987E-04 1.0714531E-02 at 120iterations finished qdiffx linear iterations at : 13:55:07 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 2.8963987E-04 1.0714531E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 13:55:08 8.264u 0.243s 0:08.78 96.8% 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 Sat Oct 15 2011 at 13:55:08 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 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: 2.524226 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): -7.488000 39.44600 ymin,ymax (A): -9.726000 42.76600 zmin,zma (A): -1.126000 62.33900 x,y,z range (A): 46.93400 52.49200 63.46500 scale (grids/A): 2.524226 object centre (A): 15.97900 16.52000 30.60650 number of atom coordinates read : 2785 total number of charged atoms : 2644 net assigned charge : 3.000026 assigned positive charge : 413.7626 centred at (gu) : 91.58043 87.62083 87.22782 assigned negative charge : -410.7635 centred at (gu) : 91.36347 87.29567 87.45068 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 148476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26890 grid for indexing accessible points = 1.400000 m= 67355 mr = 103243 m= 19036 mr = 51934 m= 3218 mr = 13844 m= 276 mr = 1993 m= 13 mr = 117 m= 0 mr = 2 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 67241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 21133 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) : 1.682817 object centre at (A) : 15.97900 16.52000 30.60650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3152905 0.3408647 midg,1,midg; midg,igrid,midg -0.1354050 -6.3991450E-02 1,midg,midg; igrid,midg,midg 2.2473073E-02 9.3939621E-03 gauss-seidel spectral radius is 0.9991778 estimated iterations to convergence 275 setup time was (sec) 1.070000 now iterating at: 13:55:09 rms-change max change #iterations 8.689704 351.4177 at 10iterations 4.981074 129.7342 at 20iterations 2.820194 62.88018 at 30iterations 1.592627 36.19733 at 40iterations 0.8960592 20.48307 at 50iterations 0.5035392 11.49123 at 60iterations 0.2822277 5.931168 at 70iterations 0.1574930 3.624991 at 80iterations 8.7999128E-02 1.937348 at 90iterations 4.9237005E-02 0.9766943 at 100iterations 2.7444091E-02 0.5756102 at 110iterations 1.5286756E-02 0.3804398 at 120iterations 8.5151587E-03 0.1720085 at 130iterations 4.7569247E-03 9.8270416E-02 at 140iterations 2.6450881E-03 6.1817169E-02 at 150iterations 1.4700065E-03 3.1196594E-02 at 160iterations 8.1934116E-04 1.7007828E-02 at 170iterations 4.5608977E-04 9.8743439E-03 at 180iterations finished qdiffx linear iterations at : 13:55:21 total time elapsed so far: 13.28000 # loops : 180 mean,max change (kT/e) : 4.5608977E-04 9.8743439E-03 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.41000 DelPhi exited at 13:55:22 13.412u 0.232s 0:13.94 97.8% 0+0k 0+0io 0pf+0w