Mon Oct 10 19:41:21 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 19:41:21 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3096 !!! WARNING: HIR 243 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: 0.5970249 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): -11.65500 44.97500 ymin,ymax (A): -18.19800 40.01400 zmin,zma (A): -13.22400 46.40500 x,y,z range (A): 56.63000 58.21200 59.62900 scale (grids/A): 0.5970249 object centre (A): 16.66000 10.90800 16.59050 number of atom coordinates read : 3096 total number of charged atoms : 2954 net assigned charge : -2.485975 assigned positive charge : 468.5659 centred at (gu) : 89.08966 89.10989 90.69693 assigned negative charge : -471.0533 centred at (gu) : 89.10396 89.06873 90.75884 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7324 nv = 96 ne = 84 npr = 61760 no. pairs analyzed = 61760 no. exposed pairs = 4296 no. arc points = 30453 no. surface atoms = 1417 nbur = 1679 mkacc time = 0.1600000 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 = 1.456000 m= 339 mr = 3519 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3041 ## 277 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9180 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3068406E-09 -4.0450368E-09 midg,1,midg; midg,igrid,midg -3.1884679E-09 5.7592392E-10 1,midg,midg; igrid,midg,midg -4.3021670E-10 -1.2322139E-09 gauss-seidel spectral radius is 0.9855340 estimated iterations to convergence 68 setup time was (sec) 0.6500000 now iterating at: 19:41:22 rms-change max change #iterations 0.1167169 18.35535 at 10iterations 9.8540718E-03 1.356285 at 20iterations 9.9135481E-04 0.1657944 at 30iterations 1.6892682E-04 3.4767151E-02 at 40iterations 4.5165900E-05 9.4470978E-03 at 50iterations finished qdiffx linear iterations at : 19:41:25 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 4.5165900E-05 9.4470978E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 19:41:26 4.511u 0.403s 0:05.21 94.2% 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 19:41:26 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3096 !!! WARNING: HIR 243 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: 1.791075 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): -11.65500 44.97500 ymin,ymax (A): -18.19800 40.01400 zmin,zma (A): -13.22400 46.40500 x,y,z range (A): 56.63000 58.21200 59.62900 scale (grids/A): 1.791075 object centre (A): 16.66000 10.90800 16.59050 number of atom coordinates read : 3096 total number of charged atoms : 2954 net assigned charge : -2.485975 assigned positive charge : 468.5659 centred at (gu) : 87.26787 87.32876 92.09015 assigned negative charge : -471.0533 centred at (gu) : 87.31187 87.20602 92.27622 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78944 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30453 grid for indexing accessible points = 1.400000 m= 26073 mr = 51119 m= 3854 mr = 17829 m= 176 mr = 2040 m= 0 mr = 47 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 457 time to turn everything in is 0.6700000 number of dielectric boundary points 38012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23023 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) : 0.5970249 object centre at (A) : 16.66000 10.90800 16.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1702097E-03 -4.4098750E-02 midg,1,midg; midg,igrid,midg 6.3290321E-03 1.7487470E-02 1,midg,midg; igrid,midg,midg 4.4227177E-03 -5.4969732E-03 gauss-seidel spectral radius is 0.9985274 estimated iterations to convergence 207 setup time was (sec) 0.9800000 now iterating at: 19:41:27 rms-change max change #iterations 4.226213 167.8975 at 10iterations 1.906803 62.13980 at 20iterations 0.8618765 28.29987 at 30iterations 0.3907408 12.21403 at 40iterations 0.1781070 5.472493 at 50iterations 8.0793418E-02 2.859133 at 60iterations 3.6621403E-02 1.192652 at 70iterations 1.6671753E-02 0.5130119 at 80iterations 7.5792652E-03 0.2249651 at 90iterations 3.4593639E-03 0.1214333 at 100iterations 1.5811687E-03 5.1492691E-02 at 110iterations 7.2983955E-04 2.3605347E-02 at 120iterations finished qdiffx linear iterations at : 19:41:37 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 7.2983955E-04 2.3605347E-02 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 19:41:37 10.634u 0.457s 0:11.39 97.2% 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 19:41:37 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3096 !!! WARNING: HIR 243 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: 2.686612 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): -11.65500 44.97500 ymin,ymax (A): -18.19800 40.01400 zmin,zma (A): -13.22400 46.40500 x,y,z range (A): 56.63000 58.21200 59.62900 scale (grids/A): 2.686612 object centre (A): 16.66000 10.90800 16.59050 number of atom coordinates read : 3096 total number of charged atoms : 2954 net assigned charge : -2.485975 assigned positive charge : 468.5659 centred at (gu) : 85.90163 85.99296 93.13516 assigned negative charge : -471.0533 centred at (gu) : 85.96761 85.80902 93.41428 start vw surface at 0.1300000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 182860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30453 grid for indexing accessible points = 1.400000 m= 84805 mr = 125757 m= 29380 mr = 65583 m= 6502 mr = 22360 m= 800 mr = 4389 m= 15 mr = 461 m= 0 mr = 2 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1680 time to turn everything in is 1.690000 number of dielectric boundary points 85810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 23631 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) : 1.791075 object centre at (A) : 16.66000 10.90800 16.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7235926E-02 -0.5955485 midg,1,midg; midg,igrid,midg 7.9672255E-02 0.3318415 1,midg,midg; igrid,midg,midg 0.1063186 -7.2734147E-02 gauss-seidel spectral radius is 0.9992502 estimated iterations to convergence 288 setup time was (sec) 2.050000 now iterating at: 19:41:40 rms-change max change #iterations 10.35647 347.8146 at 10iterations 6.121043 157.4226 at 20iterations 3.567645 77.42029 at 30iterations 2.086113 44.41505 at 40iterations 1.207691 23.89184 at 50iterations 0.6993829 14.13398 at 60iterations 0.4039187 7.376081 at 70iterations 0.2330946 4.236702 at 80iterations 0.1340392 2.352047 at 90iterations 7.7261858E-02 1.526941 at 100iterations 4.4342838E-02 0.7791510 at 110iterations 2.5493803E-02 0.4659290 at 120iterations 1.4627226E-02 0.2989349 at 130iterations 8.4072258E-03 0.1518641 at 140iterations 4.8338603E-03 8.7069511E-02 at 150iterations 2.7755350E-03 5.1092148E-02 at 160iterations 1.6064622E-03 3.2003403E-02 at 170iterations 9.3344157E-04 1.6990662E-02 at 180iterations finished qdiffx linear iterations at : 19:41:56 total time elapsed so far: 18.64000 # loops : 180 mean,max change (kT/e) : 9.3344157E-04 1.6990662E-02 energy calculations done at 18.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.80000 DelPhi exited at 19:41:57 18.802u 0.467s 0:19.91 96.7% 0+0k 0+0io 0pf+0w