Mon Oct 10 17:13:53 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 Mon Oct 10 2011 at 17:13:53 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2879 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6227151 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): 13.15300 70.32200 ymin,ymax (A): 3.522000 50.21800 zmin,zma (A): 6.524000 63.24600 x,y,z range (A): 57.16900 46.69600 56.72200 scale (grids/A): 0.6227151 object centre (A): 41.73750 26.87000 34.88500 number of atom coordinates read : 2879 total number of charged atoms : 2738 net assigned charge : -3.485967 assigned positive charge : 435.3820 centred at (gu) : 89.38393 90.65343 90.99422 assigned negative charge : -438.8692 centred at (gu) : 89.26482 90.79044 91.07698 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7542 nv = 96 ne = 84 npr = 57347 no. pairs analyzed = 57347 no. exposed pairs = 3778 no. arc points = 26690 no. surface atoms = 1278 nbur = 1601 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 3952 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.3000000 number of dielectric boundary points 3915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2680 ## 258 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9190 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0588112E-09 -1.1938941E-08 midg,1,midg; midg,igrid,midg 7.0220540E-09 -1.6292470E-08 1,midg,midg; igrid,midg,midg -1.4440039E-08 5.8506737E-09 gauss-seidel spectral radius is 0.9866756 estimated iterations to convergence 71 setup time was (sec) 0.5200000 now iterating at: 17:13:54 rms-change max change #iterations 0.1321542 18.90898 at 10iterations 1.2339073E-02 1.839455 at 20iterations 1.1554714E-03 0.1635847 at 30iterations 1.0973883E-04 1.5769958E-02 at 40iterations 1.1257866E-05 1.5296936E-03 at 50iterations finished qdiffx linear iterations at : 17:13:56 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.1257866E-05 1.5296936E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 17:13:57 3.063u 0.159s 0:03.69 86.9% 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 Mon Oct 10 2011 at 17:13:57 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2879 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.868145 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): 13.15300 70.32200 ymin,ymax (A): 3.522000 50.21800 zmin,zma (A): 6.524000 63.24600 x,y,z range (A): 57.16900 46.69600 56.72200 scale (grids/A): 1.868145 object centre (A): 41.73750 26.87000 34.88500 number of atom coordinates read : 2879 total number of charged atoms : 2738 net assigned charge : -3.485967 assigned positive charge : 435.3820 centred at (gu) : 88.15086 91.95947 92.98205 assigned negative charge : -438.8692 centred at (gu) : 87.79402 92.37125 93.23060 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26690 grid for indexing accessible points = 1.400000 m= 27834 mr = 55573 m= 3790 mr = 19892 m= 195 mr = 2108 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1517 time to turn everything in is 0.5800000 number of dielectric boundary points 36105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 215 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 21486 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) : 0.6227151 object centre at (A) : 41.73750 26.87000 34.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2122405E-03 -1.3855324E-03 midg,1,midg; midg,igrid,midg 1.1339372E-03 -2.4140097E-02 1,midg,midg; igrid,midg,midg -5.1659625E-02 2.3602873E-02 gauss-seidel spectral radius is 0.9986177 estimated iterations to convergence 213 setup time was (sec) 0.8400000 now iterating at: 17:13:58 rms-change max change #iterations 4.387921 205.4198 at 10iterations 2.041399 66.02333 at 20iterations 0.9495407 33.34137 at 30iterations 0.4417475 13.79543 at 40iterations 0.2059857 6.981049 at 50iterations 9.5564440E-02 2.939203 at 60iterations 4.4786319E-02 1.344429 at 70iterations 2.0806670E-02 0.6655159 at 80iterations 9.6865939E-03 0.2992249 at 90iterations 4.5274827E-03 0.1325378 at 100iterations 2.1050647E-03 6.4994812E-02 at 110iterations 9.8129653E-04 2.8327942E-02 at 120iterations finished qdiffx linear iterations at : 17:14:04 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 9.8129653E-04 2.8327942E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 17:14:05 6.956u 0.176s 0:08.00 89.0% 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 Mon Oct 10 2011 at 17:14:05 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2879 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.802218 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): 13.15300 70.32200 ymin,ymax (A): 3.522000 50.21800 zmin,zma (A): 6.524000 63.24600 x,y,z range (A): 57.16900 46.69600 56.72200 scale (grids/A): 2.802218 object centre (A): 41.73750 26.87000 34.88500 number of atom coordinates read : 2879 total number of charged atoms : 2738 net assigned charge : -3.485967 assigned positive charge : 435.3820 centred at (gu) : 87.22597 92.93901 94.47279 assigned negative charge : -438.8692 centred at (gu) : 86.69090 93.55674 94.84602 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 189652 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26690 grid for indexing accessible points = 1.400000 m= 92167 mr = 135551 m= 30777 mr = 74119 m= 6545 mr = 23910 m= 786 mr = 4584 m= 38 mr = 434 m= 0 mr = 6 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 4800 time to turn everything in is 1.380000 number of dielectric boundary points 81361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 21903 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) : 1.868145 object centre at (A) : 41.73750 26.87000 34.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3259405 0.2558140 midg,1,midg; midg,igrid,midg -1.3362010E-02 -0.1888165 1,midg,midg; igrid,midg,midg -0.5988465 0.3358114 gauss-seidel spectral radius is 0.9992742 estimated iterations to convergence 293 setup time was (sec) 1.670000 now iterating at: 17:14:07 rms-change max change #iterations 10.63117 456.6045 at 10iterations 6.317773 167.0931 at 20iterations 3.722551 100.7916 at 30iterations 2.187557 50.46328 at 40iterations 1.276038 26.68028 at 50iterations 0.7439401 14.47214 at 60iterations 0.4335369 8.409857 at 70iterations 0.2517883 5.180002 at 80iterations 0.1460261 2.643244 at 90iterations 8.4700167E-02 1.653049 at 100iterations 4.8973035E-02 1.042761 at 110iterations 2.8377570E-02 0.5050735 at 120iterations 1.6438503E-02 0.3083668 at 130iterations 9.5154326E-03 0.1888351 at 140iterations 5.5169887E-03 0.1019135 at 150iterations 3.1848601E-03 5.5740356E-02 at 160iterations 1.8410574E-03 3.4374237E-02 at 170iterations 1.0685230E-03 2.0874023E-02 at 180iterations finished qdiffx linear iterations at : 17:14:17 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 1.0685230E-03 2.0874023E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 17:14:18 12.058u 0.162s 0:12.71 96.0% 0+0k 0+0io 0pf+0w