Mon Oct 10 17:07:21 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+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 Mon Oct 10 2011 at 17:07:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6209772 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): -25.68600 31.64300 ymin,ymax (A): -10.75100 39.33900 zmin,zma (A): 4.805000 60.87400 x,y,z range (A): 57.32900 50.09000 56.06900 scale (grids/A): 0.6209772 object centre (A): 2.978500 14.29400 32.83950 number of atom coordinates read : 2737 total number of charged atoms : 2596 net assigned charge : -1.771969 assigned positive charge : 411.6134 centred at (gu) : 91.26292 90.47408 91.55090 assigned negative charge : -413.3864 centred at (gu) : 91.42165 90.31974 91.60319 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7236 nv = 96 ne = 84 npr = 53325 no. pairs analyzed = 53325 no. exposed pairs = 3833 no. arc points = 27152 no. surface atoms = 1285 nbur = 1452 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 3594 m= 4 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2797 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8823 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7486637E-09 -7.1866184E-09 midg,1,midg; midg,igrid,midg -1.1387038E-08 1.0821304E-08 1,midg,midg; igrid,midg,midg 7.5563209E-09 -1.7246750E-08 gauss-seidel spectral radius is 0.9865958 estimated iterations to convergence 71 setup time was (sec) 0.5300000 now iterating at: 17:07:22 rms-change max change #iterations 0.1242806 19.45617 at 10iterations 1.1641942E-02 1.766523 at 20iterations 1.0782339E-03 0.1556892 at 30iterations 1.0045408E-04 1.6979218E-02 at 40iterations 1.0354782E-05 1.5563965E-03 at 50iterations finished qdiffx linear iterations at : 17:07:25 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 1.0354782E-05 1.5563965E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 17:07:25 3.224u 0.165s 0:03.79 89.1% 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 17:07:25 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 = 2737 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 1.862931 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): -25.68600 31.64300 ymin,ymax (A): -10.75100 39.33900 zmin,zma (A): 4.805000 60.87400 x,y,z range (A): 57.32900 50.09000 56.06900 scale (grids/A): 1.862931 object centre (A): 2.978500 14.29400 32.83950 number of atom coordinates read : 2737 total number of charged atoms : 2596 net assigned charge : -1.771969 assigned positive charge : 411.6134 centred at (gu) : 93.78832 91.42151 94.65203 assigned negative charge : -413.3864 centred at (gu) : 94.26469 90.95905 94.80913 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 78296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27152 grid for indexing accessible points = 1.400000 m= 26467 mr = 51616 m= 3835 mr = 18247 m= 203 mr = 2081 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 401 time to turn everything in is 0.5500000 number of dielectric boundary points 36802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20374 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) : 0.6209772 object centre at (A) : 2.978500 14.29400 32.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7137552E-02 1.2767382E-04 midg,1,midg; midg,igrid,midg -2.4380200E-02 1.7898306E-02 1,midg,midg; igrid,midg,midg 3.1441841E-02 -6.7086868E-02 gauss-seidel spectral radius is 0.9986067 estimated iterations to convergence 212 setup time was (sec) 0.8400000 now iterating at: 17:07:26 rms-change max change #iterations 4.210438 186.8850 at 10iterations 1.948311 67.76973 at 20iterations 0.9017186 35.02570 at 30iterations 0.4175361 12.71220 at 40iterations 0.1940901 7.277050 at 50iterations 8.9630000E-02 2.582462 at 60iterations 4.1618552E-02 1.405087 at 70iterations 1.9248525E-02 0.6100235 at 80iterations 8.9391060E-03 0.2796561 at 90iterations 4.1510733E-03 0.1278629 at 100iterations 1.9254382E-03 6.1994553E-02 at 110iterations 8.9418032E-04 3.0609131E-02 at 120iterations finished qdiffx linear iterations at : 17:07:33 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 8.9418032E-04 3.0609131E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 17:07:34 7.632u 0.266s 0:08.24 95.7% 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 Mon Oct 10 2011 at 17:07:34 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 = 2737 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 2.794397 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): -25.68600 31.64300 ymin,ymax (A): -10.75100 39.33900 zmin,zma (A): 4.805000 60.87400 x,y,z range (A): 57.32900 50.09000 56.06900 scale (grids/A): 2.794397 object centre (A): 2.978500 14.29400 32.83950 number of atom coordinates read : 2737 total number of charged atoms : 2596 net assigned charge : -1.771969 assigned positive charge : 411.6134 centred at (gu) : 95.68224 92.13223 96.97783 assigned negative charge : -413.3864 centred at (gu) : 96.39699 91.43848 97.21361 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 181087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27152 grid for indexing accessible points = 1.400000 m= 87008 mr = 126040 m= 29380 mr = 68408 m= 6591 mr = 22411 m= 885 mr = 4543 m= 38 mr = 554 m= 0 mr = 13 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 1368 time to turn everything in is 1.380000 number of dielectric boundary points 83020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 20768 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) : 1.862931 object centre at (A) : 2.978500 14.29400 32.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2498028 0.1333312 midg,1,midg; midg,igrid,midg -0.2264505 0.1696140 1,midg,midg; igrid,midg,midg 0.3310909 -0.7862825 gauss-seidel spectral radius is 0.9992744 estimated iterations to convergence 293 setup time was (sec) 1.710000 now iterating at: 17:07:35 rms-change max change #iterations 10.28914 323.6595 at 10iterations 6.172486 151.6539 at 20iterations 3.657288 75.64851 at 30iterations 2.149902 52.98019 at 40iterations 1.261510 25.72955 at 50iterations 0.7353904 14.68428 at 60iterations 0.4285401 8.624096 at 70iterations 0.2492661 5.082333 at 80iterations 0.1446671 2.710302 at 90iterations 8.3703659E-02 1.691994 at 100iterations 4.8441086E-02 0.9577045 at 110iterations 2.8035382E-02 0.4938507 at 120iterations 1.6225740E-02 0.3124228 at 130iterations 9.3760872E-03 0.1731052 at 140iterations 5.4216739E-03 0.1021948 at 150iterations 3.1373315E-03 5.7579041E-02 at 160iterations 1.8105443E-03 3.5337448E-02 at 170iterations 1.0476460E-03 1.9161919E-02 at 180iterations finished qdiffx linear iterations at : 17:07:46 total time elapsed so far: 11.87000 # loops : 180 mean,max change (kT/e) : 1.0476460E-03 1.9161919E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 17:07:46 12.037u 0.259s 0:12.63 97.2% 0+0k 0+0io 0pf+0w