Tue Oct 11 03:20:22 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 03:20:22 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 = 3199 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: 0.5367346 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): 60.10600 109.9180 ymin,ymax (A): -3.203000 56.13700 zmin,zma (A): 35.89300 102.2200 x,y,z range (A): 49.81200 59.34000 66.32700 scale (grids/A): 0.5367346 object centre (A): 85.01200 26.46700 69.05650 number of atom coordinates read : 3199 total number of charged atoms : 3060 net assigned charge : -5.999974 assigned positive charge : 478.4507 centred at (gu) : 88.98390 91.61486 92.88427 assigned negative charge : -484.4519 centred at (gu) : 89.02328 91.60943 92.91351 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5777 nv = 96 ne = 84 npr = 66617 no. pairs analyzed = 66617 no. exposed pairs = 3965 no. arc points = 27158 no. surface atoms = 1343 nbur = 1856 mkacc time = 0.1700000 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 = 1.596000 m= 214 mr = 3002 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 2981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 389 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7753 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5708008E-11 -8.2826335E-10 midg,1,midg; midg,igrid,midg -1.8909921E-10 -3.3454925E-10 1,midg,midg; igrid,midg,midg -6.8962273E-11 -3.5069311E-10 gauss-seidel spectral radius is 0.9821216 estimated iterations to convergence 62 setup time was (sec) 0.6400000 now iterating at: 03:20:23 rms-change max change #iterations 6.9799453E-02 12.41319 at 10iterations 4.4934717E-03 0.7638750 at 20iterations 3.3700219E-04 6.3135147E-02 at 30iterations 3.6410664E-05 6.3859224E-03 at 40iterations 6.0065086E-06 1.1777878E-03 at 50iterations finished qdiffx linear iterations at : 03:20:27 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 6.0065086E-06 1.1777878E-03 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 03:20:28 4.861u 0.393s 0:05.93 88.5% 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 03:20:28 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 = 3199 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: 1.610204 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): 60.10600 109.9180 ymin,ymax (A): -3.203000 56.13700 zmin,zma (A): 35.89300 102.2200 x,y,z range (A): 49.81200 59.34000 66.32700 scale (grids/A): 1.610204 object centre (A): 85.01200 26.46700 69.05650 number of atom coordinates read : 3199 total number of charged atoms : 3060 net assigned charge : -5.999974 assigned positive charge : 478.4507 centred at (gu) : 86.95100 94.84357 98.65179 assigned negative charge : -484.4519 centred at (gu) : 87.06953 94.82796 98.74039 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27158 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19286 mr = 43488 m= 1975 mr = 13351 m= 37 mr = 966 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.5400000 number of dielectric boundary points 27716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 23296 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) : 0.5367346 object centre at (A) : 85.01200 26.46700 69.05650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3961173E-02 -1.3127035E-02 midg,1,midg; midg,igrid,midg -3.2594339E-03 3.5356989E-03 1,midg,midg; igrid,midg,midg -3.3557375E-03 -6.1807325E-03 gauss-seidel spectral radius is 0.9981383 estimated iterations to convergence 184 setup time was (sec) 0.8300000 now iterating at: 03:20:29 rms-change max change #iterations 3.350821 156.8327 at 10iterations 1.374965 57.07166 at 20iterations 0.5666094 28.24424 at 30iterations 0.2337162 9.040453 at 40iterations 9.6744448E-02 3.492095 at 50iterations 3.9752211E-02 1.385673 at 60iterations 1.6467908E-02 0.6014814 at 70iterations 6.7773070E-03 0.2397461 at 80iterations 2.8113050E-03 0.1067390 at 90iterations 1.1676641E-03 4.0832520E-02 at 100iterations 4.8606520E-04 1.5610695E-02 at 110iterations 2.0565221E-04 7.8182220E-03 at 120iterations finished qdiffx linear iterations at : 03:20:39 total time elapsed so far: 10.50000 # loops : 120 mean,max change (kT/e) : 2.0565221E-04 7.8182220E-03 energy calculations done at 10.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.66000 DelPhi exited at 03:20:39 10.670u 0.474s 0:11.42 97.5% 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 03:20:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3199 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: 2.415306 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): 60.10600 109.9180 ymin,ymax (A): -3.203000 56.13700 zmin,zma (A): 35.89300 102.2200 x,y,z range (A): 49.81200 59.34000 66.32700 scale (grids/A): 2.415306 object centre (A): 85.01200 26.46700 69.05650 number of atom coordinates read : 3199 total number of charged atoms : 3060 net assigned charge : -5.999974 assigned positive charge : 478.4507 centred at (gu) : 85.42622 97.26534 102.9774 assigned negative charge : -484.4519 centred at (gu) : 85.60416 97.24190 103.1103 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 149294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27158 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67598 mr = 106454 m= 18681 mr = 53606 m= 2971 mr = 14180 m= 201 mr = 1959 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 278 time to turn everything in is 1.330000 number of dielectric boundary points 62466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 24454 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) : 1.610204 object centre at (A) : 85.01200 26.46700 69.05650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4363692 -0.3297901 midg,1,midg; midg,igrid,midg 3.6781402E-03 0.1610413 1,midg,midg; igrid,midg,midg -4.2161006E-02 -8.2509838E-02 gauss-seidel spectral radius is 0.9991240 estimated iterations to convergence 267 setup time was (sec) 1.650000 now iterating at: 03:20:42 rms-change max change #iterations 8.760757 269.1547 at 10iterations 4.896278 132.9119 at 20iterations 2.724435 60.56458 at 30iterations 1.510427 34.25060 at 40iterations 0.8309221 18.04878 at 50iterations 0.4584246 10.09953 at 60iterations 0.2519515 5.485066 at 70iterations 0.1381842 2.960848 at 80iterations 7.5809889E-02 1.666445 at 90iterations 4.1430075E-02 0.8308792 at 100iterations 2.2716163E-02 0.5119534 at 110iterations 1.2446373E-02 0.2625618 at 120iterations 6.8157613E-03 0.1459961 at 130iterations 3.7253418E-03 7.5401306E-02 at 140iterations 2.0456223E-03 4.7819614E-02 at 150iterations 1.1187786E-03 2.2294998E-02 at 160iterations 6.1417191E-04 1.3369560E-02 at 170iterations 3.3779923E-04 7.2321892E-03 at 180iterations finished qdiffx linear iterations at : 03:20:57 total time elapsed so far: 17.51000 # loops : 180 mean,max change (kT/e) : 3.3779923E-04 7.2321892E-03 energy calculations done at 17.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.67000 DelPhi exited at 03:20:58 17.677u 0.454s 0:18.47 98.1% 0+0k 0+0io 0pf+0w