Mon Oct 10 14:04:27 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 14:04:27 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3176 !!! WARNING: HIR 142 has a net charge of 0.5140 !!! WARNING: HIR 143 has a net charge of 0.5140 !!! WARNING: HIY 180 has a net charge of 0.2000 !!! WARNING: ZN5 519 has a net charge of 1.4000 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: 0.5855648 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): 20.17100 80.96700 ymin,ymax (A): -26.07100 28.18100 zmin,zma (A): -6.611000 41.26500 x,y,z range (A): 60.79601 54.25200 47.87600 scale (grids/A): 0.5855648 object centre (A): 50.56900 1.054999 17.32700 number of atom coordinates read : 3176 total number of charged atoms : 3038 net assigned charge : -2.371980 assigned positive charge : 469.1991 centred at (gu) : 90.57617 89.20983 90.56470 assigned negative charge : -471.5724 centred at (gu) : 90.47918 89.19321 90.70200 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7110 nv = 96 ne = 84 npr = 65872 no. pairs analyzed = 65872 no. exposed pairs = 3777 no. arc points = 26237 no. surface atoms = 1289 nbur = 1887 mkacc time = 0.1100000 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 = 1.484000 m= 310 mr = 3936 m= 0 mr = 19 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2400000 number of dielectric boundary points 3465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2561 ## 275 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9036 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7737503E-09 -5.1656341E-09 midg,1,midg; midg,igrid,midg -1.2943402E-09 -1.2743835E-10 1,midg,midg; igrid,midg,midg -2.9377263E-09 2.3824505E-09 gauss-seidel spectral radius is 0.9849564 estimated iterations to convergence 67 setup time was (sec) 0.4400000 now iterating at: 14:04:27 rms-change max change #iterations 0.1059185 14.83507 at 10iterations 9.0763373E-03 1.327835 at 20iterations 1.0467072E-03 0.1564674 at 30iterations 2.5826233E-04 5.1330566E-02 at 40iterations 1.0736284E-04 2.1923065E-02 at 50iterations finished qdiffx linear iterations at : 14:04:30 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.0736284E-04 2.1923065E-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) 3.400000 DelPhi exited at 14:04:31 3.401u 0.146s 0:03.99 88.7% 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 Mon Oct 10 2011 at 14:04:31 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3176 !!! WARNING: HIR 142 has a net charge of 0.5140 !!! WARNING: HIR 143 has a net charge of 0.5140 !!! WARNING: HIY 180 has a net charge of 0.2000 !!! WARNING: ZN5 519 has a net charge of 1.4000 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: 1.756694 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): 20.17100 80.96700 ymin,ymax (A): -26.07100 28.18100 zmin,zma (A): -6.611000 41.26500 x,y,z range (A): 60.79601 54.25200 47.87600 scale (grids/A): 1.756694 object centre (A): 50.56900 1.054999 17.32700 number of atom coordinates read : 3176 total number of charged atoms : 3038 net assigned charge : -2.371980 assigned positive charge : 469.1991 centred at (gu) : 91.72797 87.62860 91.69357 assigned negative charge : -471.5724 centred at (gu) : 91.43764 87.57949 92.10584 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78909 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26237 grid for indexing accessible points = 1.400000 m= 25783 mr = 56007 m= 3141 mr = 18272 m= 139 mr = 1642 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 473 time to turn everything in is 0.3600000 number of dielectric boundary points 32024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 23630 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) : 0.5855648 object centre at (A) : 50.56900 1.054999 17.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1982605E-02 1.6121053E-03 midg,1,midg; midg,igrid,midg -2.0335130E-02 -1.5383277E-02 1,midg,midg; igrid,midg,midg -2.0783549E-02 1.2500802E-02 gauss-seidel spectral radius is 0.9984573 estimated iterations to convergence 202 setup time was (sec) 0.5500000 now iterating at: 14:04:32 rms-change max change #iterations 4.006577 165.1981 at 10iterations 1.794295 70.14256 at 20iterations 0.7982627 25.29681 at 30iterations 0.3578161 12.70187 at 40iterations 0.1596691 4.895417 at 50iterations 7.1399130E-02 2.578430 at 60iterations 3.2108091E-02 0.9448242 at 70iterations 1.4396322E-02 0.4453287 at 80iterations 6.4892853E-03 0.2327909 at 90iterations 2.9779230E-03 9.3540668E-02 at 100iterations 1.4056242E-03 4.6138763E-02 at 110iterations 7.2785828E-04 2.7641296E-02 at 120iterations finished qdiffx linear iterations at : 14:04:38 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 7.2785828E-04 2.7641296E-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) 7.630000 DelPhi exited at 14:04:39 7.633u 0.221s 0:08.19 95.8% 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 Mon Oct 10 2011 at 14:04:39 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3176 !!! WARNING: HIR 142 has a net charge of 0.5140 !!! WARNING: HIR 143 has a net charge of 0.5140 !!! WARNING: HIY 180 has a net charge of 0.2000 !!! WARNING: ZN5 519 has a net charge of 1.4000 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: 2.635041 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): 20.17100 80.96700 ymin,ymax (A): -26.07100 28.18100 zmin,zma (A): -6.611000 41.26500 x,y,z range (A): 60.79601 54.25200 47.87600 scale (grids/A): 2.635041 object centre (A): 50.56900 1.054999 17.32700 number of atom coordinates read : 3176 total number of charged atoms : 3038 net assigned charge : -2.371980 assigned positive charge : 469.1991 centred at (gu) : 92.59174 86.44257 92.54024 assigned negative charge : -471.5724 centred at (gu) : 92.15643 86.36928 93.15857 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 183526 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26237 grid for indexing accessible points = 1.400000 m= 87621 mr = 136495 m= 27029 mr = 70689 m= 5115 mr = 20732 m= 588 mr = 3427 m= 25 mr = 329 m= 0 mr = 6 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1624 time to turn everything in is 0.9500000 number of dielectric boundary points 72226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 24299 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) : 1.756694 object centre at (A) : 50.56900 1.054999 17.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2927314 2.4782697E-02 midg,1,midg; midg,igrid,midg -0.1901344 -0.1338147 1,midg,midg; igrid,midg,midg -0.2856718 0.3254048 gauss-seidel spectral radius is 0.9992154 estimated iterations to convergence 282 setup time was (sec) 1.170000 now iterating at: 14:04:40 rms-change max change #iterations 9.893742 297.2360 at 10iterations 5.748166 140.3916 at 20iterations 3.311637 78.74377 at 30iterations 1.901920 48.41301 at 40iterations 1.087529 20.94216 at 50iterations 0.6217465 13.70870 at 60iterations 0.3543589 7.271517 at 70iterations 0.2017049 3.587508 at 80iterations 0.1144779 2.177178 at 90iterations 6.5046936E-02 1.233337 at 100iterations 3.6976650E-02 0.7194042 at 110iterations 2.1000704E-02 0.3827348 at 120iterations 1.1906900E-02 0.2130089 at 130iterations 6.7891725E-03 0.1332450 at 140iterations 3.8667310E-03 7.6288104E-02 at 150iterations 2.2292358E-03 5.2019119E-02 at 160iterations 1.3030040E-03 2.5535583E-02 at 170iterations 7.9017034E-04 1.8178940E-02 at 180iterations finished qdiffx linear iterations at : 14:04:52 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 7.9017034E-04 1.8178940E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 14:04:52 12.457u 0.210s 0:13.00 97.3% 0+0k 0+0io 0pf+0w