Tue Nov 22 14:11:10 PST 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 Nov 22 2011 at 14:11:15 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5858057 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): -25.52800 35.24300 ymin,ymax (A): -18.88200 20.72100 zmin,zma (A): -3.423000 38.44600 x,y,z range (A): 60.77100 39.60300 41.86900 scale (grids/A): 0.5858057 object centre (A): 4.857500 0.9194994 17.51150 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.99396 90.20969 90.58620 assigned negative charge : -284.8263 centred at (gu) : 90.01917 90.28554 90.70400 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4519 nv = 96 ne = 84 npr = 40465 no. pairs analyzed = 40465 no. exposed pairs = 2453 no. arc points = 17330 no. surface atoms = 832 nbur = 1132 mkacc time = 9.0000004E-02 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= 187 mr = 2404 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2100000 number of dielectric boundary points 2287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1810 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5554 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4460272E-09 -1.4089914E-09 midg,1,midg; midg,igrid,midg 2.0026247E-09 -5.1426763E-10 1,midg,midg; igrid,midg,midg 1.2498163E-09 3.8694073E-10 gauss-seidel spectral radius is 0.9848719 estimated iterations to convergence 67 setup time was (sec) 0.4300000 now iterating at: 14:11:18 rms-change max change #iterations 8.1404567E-02 14.36861 at 10iterations 6.5352852E-03 1.263486 at 20iterations 5.2096328E-04 8.9023829E-02 at 30iterations 4.1015257E-05 8.3923340E-03 at 40iterations 3.3072236E-06 6.1035156E-04 at 50iterations finished qdiffx linear iterations at : 14:11:26 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 3.3072236E-06 6.1035156E-04 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 14:11:28 3.047u 0.154s 0:13.60 23.4% 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 Nov 22 2011 at 14:11:30 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.757417 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): -25.52800 35.24300 ymin,ymax (A): -18.88200 20.72100 zmin,zma (A): -3.423000 38.44600 x,y,z range (A): 60.77100 39.60300 41.86900 scale (grids/A): 1.757417 object centre (A): 4.857500 0.9194994 17.51150 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.98179 90.62894 91.75864 assigned negative charge : -284.8263 centred at (gu) : 90.05768 90.85680 92.11218 start vw surface at 0.1300000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 48923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17330 grid for indexing accessible points = 1.400000 m= 16705 mr = 33169 m= 1990 mr = 12453 m= 60 mr = 1139 m= 0 mr = 23 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1589 time to turn everything in is 0.3600000 number of dielectric boundary points 20894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14239 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) : 0.5858057 object centre at (A) : 4.857500 0.9194994 17.51150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0128425E-03 -5.3075752E-03 midg,1,midg; midg,igrid,midg 2.8794354E-03 -1.3390189E-03 1,midg,midg; igrid,midg,midg 3.4202654E-02 2.2007573E-02 gauss-seidel spectral radius is 0.9983206 estimated iterations to convergence 194 setup time was (sec) 0.6200000 now iterating at: 14:11:32 rms-change max change #iterations 3.037893 175.8974 at 10iterations 1.304907 56.39743 at 20iterations 0.5617129 24.18096 at 30iterations 0.2419245 10.59647 at 40iterations 0.1039404 4.117959 at 50iterations 4.4956584E-02 1.736780 at 60iterations 1.9361477E-02 0.7956934 at 70iterations 8.3231712E-03 0.3266640 at 80iterations 3.5831532E-03 0.1584119 at 90iterations 1.5430041E-03 5.9993744E-02 at 100iterations 6.6510518E-04 2.5796413E-02 at 110iterations 2.8809087E-04 1.0654449E-02 at 120iterations finished qdiffx linear iterations at : 14:11:51 total time elapsed so far: 6.660000 # loops : 120 mean,max change (kT/e) : 2.8809087E-04 1.0654449E-02 energy calculations done at 6.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.840000 DelPhi exited at 14:11:56 6.842u 0.197s 0:26.25 26.7% 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 Tue Nov 22 2011 at 14:11:58 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.636126 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): -25.52800 35.24300 ymin,ymax (A): -18.88200 20.72100 zmin,zma (A): -3.423000 38.44600 x,y,z range (A): 60.77100 39.60300 41.86900 scale (grids/A): 2.636126 object centre (A): 4.857500 0.9194994 17.51150 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.97272 90.94352 92.63802 assigned negative charge : -284.8263 centred at (gu) : 90.08657 91.28524 93.16830 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 113158 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17330 grid for indexing accessible points = 1.400000 m= 55979 mr = 80578 m= 18302 mr = 46090 m= 3216 mr = 14672 m= 243 mr = 2311 m= 9 mr = 148 m= 0 mr = 2 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 5477 time to turn everything in is 0.8500000 number of dielectric boundary points 47106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 14648 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) : 1.757417 object centre at (A) : 4.857500 0.9194994 17.51150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6787316E-02 -5.4364372E-02 midg,1,midg; midg,igrid,midg 2.3471512E-02 -9.1749653E-03 1,midg,midg; igrid,midg,midg 0.4017152 0.2408486 gauss-seidel spectral radius is 0.9991500 estimated iterations to convergence 271 setup time was (sec) 1.150000 now iterating at: 14:12:06 rms-change max change #iterations 7.424415 267.4393 at 10iterations 4.131910 121.9195 at 20iterations 2.298487 56.34097 at 30iterations 1.268197 30.31598 at 40iterations 0.7002349 16.61740 at 50iterations 0.3851890 9.171833 at 60iterations 0.2119297 4.908505 at 70iterations 0.1167290 2.700713 at 80iterations 6.4130358E-02 1.507385 at 90iterations 3.5381343E-02 0.8453102 at 100iterations 1.9489959E-02 0.4411240 at 110iterations 1.0762336E-02 0.2438622 at 120iterations 5.9183971E-03 0.1420441 at 130iterations 3.2474741E-03 7.3067904E-02 at 140iterations 1.7915248E-03 4.2291164E-02 at 150iterations 9.8631810E-04 2.4700165E-02 at 160iterations 5.4277480E-04 1.2161255E-02 at 170iterations 2.9866159E-04 7.4234009E-03 at 180iterations finished qdiffx linear iterations at : 14:12:33 total time elapsed so far: 10.75000 # loops : 180 mean,max change (kT/e) : 2.9866159E-04 7.4234009E-03 energy calculations done at 10.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.92000 DelPhi exited at 14:12:36 10.922u 0.206s 0:38.49 28.8% 0+0k 0+0io 0pf+0w