Sat Oct 8 11:36:26 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 Sat Oct 8 2011 at 11:36:26 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4364 !!! WARNING: HIR 437 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: 0.5666083 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): 60.06000 115.6130 ymin,ymax (A): 20.75100 83.14200 zmin,zma (A): -7.689000 55.14100 x,y,z range (A): 55.55300 62.39100 62.83000 scale (grids/A): 0.5666083 object centre (A): 87.83650 51.94650 23.72600 number of atom coordinates read : 4364 total number of charged atoms : 4216 net assigned charge : -1.985943 assigned positive charge : 658.5123 centred at (gu) : 89.52071 90.10909 89.80956 assigned negative charge : -660.5013 centred at (gu) : 89.72409 90.06890 89.64335 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8894 nv = 96 ne = 84 npr = 91634 no. pairs analyzed = 91634 no. exposed pairs = 4924 no. arc points = 33403 no. surface atoms = 1655 nbur = 2709 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 = 1.512000 m= 385 mr = 5164 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.3100000 number of dielectric boundary points 4080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3507 ## 446 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11888 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9835384E-09 2.9660350E-09 midg,1,midg; midg,igrid,midg -1.0884966E-09 5.6830352E-10 1,midg,midg; igrid,midg,midg 4.3243520E-09 -4.1053703E-09 gauss-seidel spectral radius is 0.9840280 estimated iterations to convergence 65 setup time was (sec) 0.5200000 now iterating at: 11:36:27 rms-change max change #iterations 0.1103602 20.49141 at 10iterations 8.6708535E-03 1.372548 at 20iterations 1.1215272E-03 0.1438456 at 30iterations 3.2461504E-04 4.4322968E-02 at 40iterations 1.1558086E-04 1.6460419E-02 at 50iterations finished qdiffx linear iterations at : 11:36:30 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 1.1558086E-04 1.6460419E-02 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 11:36:31 3.824u 0.216s 0:04.34 92.8% 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 Sat Oct 8 2011 at 11:36:31 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4364 !!! WARNING: HIR 437 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: 1.699825 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): 60.06000 115.6130 ymin,ymax (A): 20.75100 83.14200 zmin,zma (A): -7.689000 55.14100 x,y,z range (A): 55.55300 62.39100 62.83000 scale (grids/A): 1.699825 object centre (A): 87.83650 51.94650 23.72600 number of atom coordinates read : 4364 total number of charged atoms : 4216 net assigned charge : -1.985943 assigned positive charge : 658.5123 centred at (gu) : 88.56094 90.32585 89.42742 assigned negative charge : -660.5013 centred at (gu) : 89.17204 90.20619 88.92962 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 100125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33403 grid for indexing accessible points = 1.400000 m= 34161 mr = 72627 m= 4260 mr = 25281 m= 127 mr = 2486 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 6463 time to turn everything in is 0.4900000 number of dielectric boundary points 38263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 32548 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) : 0.5666083 object centre at (A) : 87.83650 51.94650 23.72600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8393587E-02 2.5542755E-02 midg,1,midg; midg,igrid,midg -3.1814985E-02 3.3970699E-02 1,midg,midg; igrid,midg,midg 3.8966514E-02 -3.5665099E-02 gauss-seidel spectral radius is 0.9984577 estimated iterations to convergence 202 setup time was (sec) 0.7400000 now iterating at: 11:36:32 rms-change max change #iterations 4.522601 158.1245 at 10iterations 2.023027 63.04964 at 20iterations 0.9064823 26.19867 at 30iterations 0.4046565 12.85886 at 40iterations 0.1812601 5.753475 at 50iterations 8.1029452E-02 2.332428 at 60iterations 3.6401764E-02 1.002720 at 70iterations 1.6342068E-02 0.4659142 at 80iterations 7.3571028E-03 0.2218513 at 90iterations 3.3492988E-03 9.4631195E-02 at 100iterations 1.5561458E-03 4.4525146E-02 at 110iterations 7.4648875E-04 2.0584106E-02 at 120iterations finished qdiffx linear iterations at : 11:36:40 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 7.4648875E-04 2.0584106E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.050000 DelPhi exited at 11:36:40 9.051u 0.254s 0:09.64 96.4% 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 Sat Oct 8 2011 at 11:36:40 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4364 !!! WARNING: HIR 437 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: 2.549737 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): 60.06000 115.6130 ymin,ymax (A): 20.75100 83.14200 zmin,zma (A): -7.689000 55.14100 x,y,z range (A): 55.55300 62.39100 62.83000 scale (grids/A): 2.549737 object centre (A): 87.83650 51.94650 23.72600 number of atom coordinates read : 4364 total number of charged atoms : 4216 net assigned charge : -1.985943 assigned positive charge : 658.5123 centred at (gu) : 87.84113 90.48852 89.14064 assigned negative charge : -660.5013 centred at (gu) : 88.75784 90.30909 88.39423 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 232434 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33403 grid for indexing accessible points = 1.400000 m= 115486 mr = 175890 m= 36617 mr = 95269 m= 7112 mr = 29233 m= 556 mr = 5267 m= 11 mr = 247 m= 0 mr = 3 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 22106 time to turn everything in is 1.260000 number of dielectric boundary points 86307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 33699 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) : 1.699825 object centre at (A) : 87.83650 51.94650 23.72600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3738518 0.2626750 midg,1,midg; midg,igrid,midg -0.8488636 0.7034572 1,midg,midg; igrid,midg,midg 0.6571773 -0.4351827 gauss-seidel spectral radius is 0.9992406 estimated iterations to convergence 286 setup time was (sec) 1.550000 now iterating at: 11:36:42 rms-change max change #iterations 11.31610 291.6954 at 10iterations 6.586223 154.9362 at 20iterations 3.815253 75.20467 at 30iterations 2.210531 40.70810 at 40iterations 1.274048 22.80886 at 50iterations 0.7305580 12.64746 at 60iterations 0.4203458 6.929285 at 70iterations 0.2410126 4.304691 at 80iterations 0.1376825 2.513020 at 90iterations 7.8969993E-02 1.285582 at 100iterations 4.5245972E-02 0.7243347 at 110iterations 2.5925495E-02 0.4166498 at 120iterations 1.4818725E-02 0.2600036 at 130iterations 8.4867952E-03 0.1446705 at 140iterations 4.8870882E-03 8.1153870E-02 at 150iterations 2.8315550E-03 5.0765991E-02 at 160iterations 1.6559125E-03 2.8936386E-02 at 170iterations 9.8586536E-04 1.6574860E-02 at 180iterations finished qdiffx linear iterations at : 11:36:56 total time elapsed so far: 15.28000 # loops : 180 mean,max change (kT/e) : 9.8586536E-04 1.6574860E-02 energy calculations done at 15.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.42000 DelPhi exited at 11:36:56 15.420u 0.287s 0:16.10 97.5% 0+0k 0+0io 0pf+0w