Sun Oct 9 01:48:07 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 Sun Oct 9 2011 at 01:48:08 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5849779 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): -40.85400 16.39000 ymin,ymax (A): -11.99200 48.72900 zmin,zma (A): -51.49300 9.364000 x,y,z range (A): 57.24400 60.72100 60.85700 scale (grids/A): 0.5849779 object centre (A): -12.23200 18.36850 -21.06450 number of atom coordinates read : 3341 total number of charged atoms : 3198 net assigned charge : 11.22604 assigned positive charge : 497.8526 centred at (gu) : 89.70349 90.44743 92.46758 assigned negative charge : -486.6282 centred at (gu) : 89.81712 90.38833 92.71384 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7847 nv = 96 ne = 84 npr = 64981 no. pairs analyzed = 64981 no. exposed pairs = 4458 no. arc points = 32083 no. surface atoms = 1479 nbur = 1862 mkacc time = 0.1400000 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= 351 mr = 4000 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3600000 number of dielectric boundary points 4168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3335 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5672236E-09 -7.5052977E-09 midg,1,midg; midg,igrid,midg 1.2756411E-09 5.2393632E-09 1,midg,midg; igrid,midg,midg 6.6726620E-09 -1.4278571E-10 gauss-seidel spectral radius is 0.9849588 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 01:48:08 rms-change max change #iterations 0.1079312 21.84874 at 10iterations 8.5885320E-03 1.172981 at 20iterations 7.1927835E-04 0.1144295 at 30iterations 6.6800727E-05 9.0961456E-03 at 40iterations 8.6863301E-06 9.3364716E-04 at 50iterations finished qdiffx linear iterations at : 01:48:11 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 8.6863301E-06 9.3364716E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 01:48:12 3.512u 0.234s 0:04.14 90.3% 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 Sun Oct 9 2011 at 01:48:12 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.754934 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): -40.85400 16.39000 ymin,ymax (A): -11.99200 48.72900 zmin,zma (A): -51.49300 9.364000 x,y,z range (A): 57.24400 60.72100 60.85700 scale (grids/A): 1.754934 object centre (A): -12.23200 18.36850 -21.06450 number of atom coordinates read : 3341 total number of charged atoms : 3198 net assigned charge : 11.22604 assigned positive charge : 497.8526 centred at (gu) : 89.10973 91.34138 97.40164 assigned negative charge : -486.6282 centred at (gu) : 89.45087 91.16468 98.14136 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32083 grid for indexing accessible points = 1.400000 m= 27941 mr = 57784 m= 3456 mr = 19331 m= 124 mr = 1843 m= 0 mr = 12 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 0.6100000 number of dielectric boundary points 38576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 304 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 24906 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) : 0.5849779 object centre at (A) : -12.23200 18.36850 -21.06450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0409079E-02 -3.1305244E-03 midg,1,midg; midg,igrid,midg 3.1346958E-02 5.3594764E-02 1,midg,midg; igrid,midg,midg 1.4941720E-02 -7.8360941E-03 gauss-seidel spectral radius is 0.9984852 estimated iterations to convergence 204 setup time was (sec) 0.9200000 now iterating at: 01:48:13 rms-change max change #iterations 4.182710 178.9120 at 10iterations 1.861952 65.34180 at 20iterations 0.8330483 27.83621 at 30iterations 0.3735879 12.71074 at 40iterations 0.1682621 5.260617 at 50iterations 7.5551838E-02 2.549333 at 60iterations 3.3797976E-02 1.028389 at 70iterations 1.5211724E-02 0.4606795 at 80iterations 6.8320027E-03 0.2186794 at 90iterations 3.0686932E-03 0.1136627 at 100iterations 1.3842101E-03 4.3748617E-02 at 110iterations 6.2197313E-04 2.2656441E-02 at 120iterations finished qdiffx linear iterations at : 01:48:20 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 6.2197313E-04 2.2656441E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 01:48:20 7.834u 0.251s 0:08.37 96.5% 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 Sun Oct 9 2011 at 01:48:20 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.632401 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): -40.85400 16.39000 ymin,ymax (A): -11.99200 48.72900 zmin,zma (A): -51.49300 9.364000 x,y,z range (A): 57.24400 60.72100 60.85700 scale (grids/A): 2.632401 object centre (A): -12.23200 18.36850 -21.06450 number of atom coordinates read : 3341 total number of charged atoms : 3198 net assigned charge : 11.22604 assigned positive charge : 497.8526 centred at (gu) : 88.66436 92.01183 101.1025 assigned negative charge : -486.6282 centred at (gu) : 89.17633 91.74701 102.2120 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 199233 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32083 grid for indexing accessible points = 1.400000 m= 94059 mr = 141033 m= 29757 mr = 74296 m= 5789 mr = 22714 m= 550 mr = 3923 m= 15 mr = 270 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 3071 time to turn everything in is 1.430000 number of dielectric boundary points 87166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 25559 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) : 1.754934 object centre at (A) : -12.23200 18.36850 -21.06450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3958750 -7.3816583E-02 midg,1,midg; midg,igrid,midg 0.5863156 0.7749908 1,midg,midg; igrid,midg,midg 0.1479488 -3.0986570E-02 gauss-seidel spectral radius is 0.9992494 estimated iterations to convergence 288 setup time was (sec) 1.760000 now iterating at: 01:48:22 rms-change max change #iterations 10.34528 270.9189 at 10iterations 6.080604 147.8138 at 20iterations 3.545008 81.78800 at 30iterations 2.063046 53.00745 at 40iterations 1.190708 24.10848 at 50iterations 0.6873047 13.34854 at 60iterations 0.3960694 7.875196 at 70iterations 0.2277113 4.339176 at 80iterations 0.1308158 2.243111 at 90iterations 7.5035259E-02 1.590942 at 100iterations 4.3068480E-02 0.8515120 at 110iterations 2.4640370E-02 0.4239769 at 120iterations 1.4104038E-02 0.2517033 at 130iterations 8.1012864E-03 0.1384735 at 140iterations 4.6349117E-03 8.7165833E-02 at 150iterations 2.6503841E-03 4.5700073E-02 at 160iterations 1.5162183E-03 2.5144577E-02 at 170iterations 8.6800352E-04 1.5130043E-02 at 180iterations finished qdiffx linear iterations at : 01:48:32 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 8.6800352E-04 1.5130043E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 01:48:33 12.061u 0.199s 0:12.59 97.2% 0+0k 0+0io 0pf+0w