Sat Oct 8 17:06:16 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 17:06:16 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5287547 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): -54.84900 12.47900 ymin,ymax (A): 21.08600 82.83400 zmin,zma (A): 40.73200 96.67000 x,y,z range (A): 67.32800 61.74800 55.93800 scale (grids/A): 0.5287547 object centre (A): -21.18500 51.96000 68.70100 number of atom coordinates read : 3527 total number of charged atoms : 3381 net assigned charge : -2.999988 assigned positive charge : 538.6590 centred at (gu) : 91.22788 90.25814 90.13333 assigned negative charge : -541.6609 centred at (gu) : 91.26592 90.22971 90.14792 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6280 nv = 96 ne = 84 npr = 71439 no. pairs analyzed = 71439 no. exposed pairs = 4397 no. arc points = 30172 no. surface atoms = 1493 nbur = 2034 mkacc time = 0.2000000 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= 237 mr = 3302 m= 0 mr = 8 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3095 ## 441 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8392 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9669649E-11 -1.5706132E-10 midg,1,midg; midg,igrid,midg -1.9643430E-10 2.8800556E-11 1,midg,midg; igrid,midg,midg 4.7363388E-11 -3.4278794E-10 gauss-seidel spectral radius is 0.9816093 estimated iterations to convergence 61 setup time was (sec) 0.7000000 now iterating at: 17:06:17 rms-change max change #iterations 6.8079166E-02 10.34525 at 10iterations 4.2738756E-03 0.6417046 at 20iterations 3.2380479E-04 4.8008010E-02 at 30iterations 4.8340400E-05 1.0375023E-02 at 40iterations 1.0641938E-05 2.4971962E-03 at 50iterations finished qdiffx linear iterations at : 17:06:21 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.0641938E-05 2.4971962E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 17:06:21 4.245u 0.269s 0:04.80 93.7% 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 Sat Oct 8 2011 at 17:06:21 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.586264 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): -54.84900 12.47900 ymin,ymax (A): 21.08600 82.83400 zmin,zma (A): 40.73200 96.67000 x,y,z range (A): 67.32800 61.74800 55.93800 scale (grids/A): 1.586264 object centre (A): -21.18500 51.96000 68.70100 number of atom coordinates read : 3527 total number of charged atoms : 3381 net assigned charge : -2.999988 assigned positive charge : 538.6590 centred at (gu) : 93.68253 90.77329 90.39886 assigned negative charge : -541.6609 centred at (gu) : 93.79749 90.68904 90.44332 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 69850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30172 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21334 mr = 47861 m= 2075 mr = 14595 m= 65 mr = 982 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.6500000 number of dielectric boundary points 29884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 386 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 25662 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) : 0.5287547 object centre at (A) : -21.18500 51.96000 68.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8603462E-03 -7.6187183E-03 midg,1,midg; midg,igrid,midg -1.2357626E-02 1.2062477E-03 1,midg,midg; igrid,midg,midg 7.9012364E-03 2.4453879E-03 gauss-seidel spectral radius is 0.9981230 estimated iterations to convergence 183 setup time was (sec) 0.9400000 now iterating at: 17:06:22 rms-change max change #iterations 3.459340 167.4446 at 10iterations 1.415702 67.04822 at 20iterations 0.5821359 20.81456 at 30iterations 0.2396502 9.251947 at 40iterations 9.8901615E-02 3.948101 at 50iterations 4.0718906E-02 1.444210 at 60iterations 1.6765943E-02 0.5879374 at 70iterations 6.9168406E-03 0.2472897 at 80iterations 2.8581065E-03 0.1063385 at 90iterations 1.1933108E-03 4.2676926E-02 at 100iterations 4.9756229E-04 1.6645432E-02 at 110iterations 2.1237053E-04 7.5950623E-03 at 120iterations finished qdiffx linear iterations at : 17:06:31 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 2.1237053E-04 7.5950623E-03 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 17:06:31 9.479u 0.322s 0:10.07 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 Sat Oct 8 2011 at 17:06:31 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.379396 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): -54.84900 12.47900 ymin,ymax (A): 21.08600 82.83400 zmin,zma (A): 40.73200 96.67000 x,y,z range (A): 67.32800 61.74800 55.93800 scale (grids/A): 2.379396 object centre (A): -21.18500 51.96000 68.70100 number of atom coordinates read : 3527 total number of charged atoms : 3381 net assigned charge : -2.999988 assigned positive charge : 538.6590 centred at (gu) : 95.52345 91.15962 90.59821 assigned negative charge : -541.6609 centred at (gu) : 95.69624 91.03345 90.66495 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 162569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30172 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 74860 mr = 117537 m= 20525 mr = 59127 m= 3161 mr = 15255 m= 189 mr = 1965 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 222 time to turn everything in is 1.550000 number of dielectric boundary points 67346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 27007 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) : 1.586264 object centre at (A) : -21.18500 51.96000 68.70100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5824305E-02 -9.7554967E-02 midg,1,midg; midg,igrid,midg -0.1795701 4.8133489E-02 1,midg,midg; igrid,midg,midg 2.0061731E-02 0.1819749 gauss-seidel spectral radius is 0.9991258 estimated iterations to convergence 267 setup time was (sec) 1.890000 now iterating at: 17:06:33 rms-change max change #iterations 9.144324 434.3423 at 10iterations 5.134916 121.8769 at 20iterations 2.865967 67.40662 at 30iterations 1.591320 33.27933 at 40iterations 0.8796888 19.86794 at 50iterations 0.4855596 10.78135 at 60iterations 0.2672899 5.925924 at 70iterations 0.1471871 3.129687 at 80iterations 8.0839492E-02 1.710731 at 90iterations 4.4438731E-02 0.9579787 at 100iterations 2.4393650E-02 0.4757112 at 110iterations 1.3393719E-02 0.2800653 at 120iterations 7.3351534E-03 0.1446705 at 130iterations 4.0404648E-03 8.3604813E-02 at 140iterations 2.2142809E-03 4.4967651E-02 at 150iterations 1.2180993E-03 2.8852463E-02 at 160iterations 6.7203940E-04 1.3240457E-02 at 170iterations 3.7318337E-04 7.6103210E-03 at 180iterations finished qdiffx linear iterations at : 17:06:47 total time elapsed so far: 15.63000 # loops : 180 mean,max change (kT/e) : 3.7318337E-04 7.6103210E-03 energy calculations done at 15.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.82000 DelPhi exited at 17:06:48 15.818u 0.331s 0:16.43 98.2% 0+0k 0+0io 0pf+0w