Tue Oct 11 06:32:36 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 06:32:36 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 = 2089 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: 0.7183647 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): -40.95000 -0.6990000 ymin,ymax (A): -27.14600 18.75800 zmin,zma (A): -14.89600 34.66100 x,y,z range (A): 40.25100 45.90400 49.55700 scale (grids/A): 0.7183647 object centre (A): -20.82450 -4.194000 9.882500 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 91.25719 89.84577 88.93552 assigned negative charge : -311.0742 centred at (gu) : 91.30500 89.98056 88.87674 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7300 nv = 96 ne = 84 npr = 41788 no. pairs analyzed = 41788 no. exposed pairs = 2554 no. arc points = 17385 no. surface atoms = 869 nbur = 1220 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 4189 m= 5 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1604 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8008 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1370747E-08 8.8309065E-08 midg,1,midg; midg,igrid,midg 1.5913110E-07 -1.3484839E-08 1,midg,midg; igrid,midg,midg 7.9881659E-08 5.1684417E-08 gauss-seidel spectral radius is 0.9898958 estimated iterations to convergence 81 setup time was (sec) 0.5200000 now iterating at: 06:32:37 rms-change max change #iterations 0.2130081 29.35512 at 10iterations 2.7139558E-02 4.087381 at 20iterations 3.6685627E-03 0.5092583 at 30iterations 5.5323320E-04 7.3713303E-02 at 40iterations 1.1629380E-04 1.5432358E-02 at 50iterations finished qdiffx linear iterations at : 06:32:40 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.1629380E-04 1.5432358E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:32:40 3.338u 0.153s 0:03.98 87.4% 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 06:32:40 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 = 2089 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: 2.155094 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): -40.95000 -0.6990000 ymin,ymax (A): -27.14600 18.75800 zmin,zma (A): -14.89600 34.66100 x,y,z range (A): 40.25100 45.90400 49.55700 scale (grids/A): 2.155094 object centre (A): -20.82450 -4.194000 9.882500 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 93.77142 89.53760 86.80640 assigned negative charge : -311.0742 centred at (gu) : 93.91508 89.94179 86.63033 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77578 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17385 grid for indexing accessible points = 1.400000 m= 31254 mr = 55296 m= 6158 mr = 23702 m= 593 mr = 4061 m= 16 mr = 307 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 32233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15579 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) : 0.7183647 object centre at (A) : -20.82450 -4.194000 9.882500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1489609E-02 4.1431401E-02 midg,1,midg; midg,igrid,midg 4.9228996E-02 1.5877539E-02 1,midg,midg; igrid,midg,midg 1.5148097E-02 3.3776447E-02 gauss-seidel spectral radius is 0.9988614 estimated iterations to convergence 235 setup time was (sec) 0.9200000 now iterating at: 06:32:42 rms-change max change #iterations 4.740550 186.0727 at 10iterations 2.372492 73.25626 at 20iterations 1.193821 39.55418 at 30iterations 0.5971328 18.24468 at 40iterations 0.2998040 8.869426 at 50iterations 0.1503602 4.616398 at 60iterations 7.5147808E-02 2.211477 at 70iterations 3.7727408E-02 1.127330 at 80iterations 1.9031134E-02 0.5813103 at 90iterations 9.5518045E-03 0.2801611 at 100iterations 4.8335288E-03 0.1599197 at 110iterations 2.4534198E-03 7.6374054E-02 at 120iterations finished qdiffx linear iterations at : 06:32:48 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 2.4534198E-03 7.6374054E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 06:32:49 7.698u 0.156s 0:08.34 94.0% 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 Tue Oct 11 2011 at 06:32:49 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 = 2089 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: 3.232641 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): -40.95000 -0.6990000 ymin,ymax (A): -27.14600 18.75800 zmin,zma (A): -14.89600 34.66100 x,y,z range (A): 40.25100 45.90400 49.55700 scale (grids/A): 3.232641 object centre (A): -20.82450 -4.194000 9.882500 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 95.65701 89.30627 85.20969 assigned negative charge : -311.0742 centred at (gu) : 95.87258 89.91267 84.94564 start vw surface at 0.1600000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 178486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17385 grid for indexing accessible points = 1.400000 m= 97345 mr = 132741 m= 39782 mr = 81228 m= 11686 mr = 32547 m= 2389 mr = 9048 m= 301 mr = 1662 m= 8 mr = 196 m= 0 mr = 3 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.940000 number of dielectric boundary points 72572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 15688 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) : 2.155094 object centre at (A) : -20.82450 -4.194000 9.882500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3390462 0.1808673 midg,1,midg; midg,igrid,midg 0.3804115 0.1995520 1,midg,midg; igrid,midg,midg 8.9279458E-02 0.3440369 gauss-seidel spectral radius is 0.9993055 estimated iterations to convergence 299 setup time was (sec) 2.260000 now iterating at: 06:32:51 rms-change max change #iterations 10.48576 318.3441 at 10iterations 6.221824 194.0806 at 20iterations 3.685013 72.85699 at 30iterations 2.176812 38.35849 at 40iterations 1.287191 23.92585 at 50iterations 0.7559246 14.33290 at 60iterations 0.4456226 7.380619 at 70iterations 0.2619747 4.671373 at 80iterations 0.1544247 2.856465 at 90iterations 9.0620413E-02 1.557036 at 100iterations 5.3333357E-02 0.8996563 at 110iterations 3.1461645E-02 0.5313721 at 120iterations 1.8651722E-02 0.3156419 at 130iterations 1.1153459E-02 0.2043991 at 140iterations 6.7819417E-03 0.1143665 at 150iterations 4.2254822E-03 7.5450897E-02 at 160iterations 2.7506170E-03 5.5076599E-02 at 170iterations 1.8874741E-03 3.3477783E-02 at 180iterations finished qdiffx linear iterations at : 06:33:02 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 1.8874741E-03 3.3477783E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 06:33:02 12.784u 0.224s 0:13.46 96.5% 0+0k 0+0io 0pf+0w