Mon Oct 10 09:25:37 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 Mon Oct 10 2011 at 09:25:37 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: 235 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2229 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5326231 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): -19.91700 46.92200 ymin,ymax (A): -19.54700 25.38200 zmin,zma (A): -18.14600 38.10800 x,y,z range (A): 66.83900 44.92900 56.25400 scale (grids/A): 0.5326231 object centre (A): 13.50250 2.917500 9.981001 number of atom coordinates read : 2229 total number of charged atoms : 2093 net assigned charge : -0.9999955 assigned positive charge : 334.8683 centred at (gu) : 90.84893 89.55849 87.63191 assigned negative charge : -335.8689 centred at (gu) : 90.80521 89.53246 87.66903 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4226 nv = 96 ne = 84 npr = 43515 no. pairs analyzed = 43515 no. exposed pairs = 3053 no. arc points = 21932 no. surface atoms = 1037 nbur = 1192 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 = 1.596000 m= 163 mr = 2030 m= 0 mr = 5 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2268 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 5506 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3247796E-10 -8.3431997E-11 midg,1,midg; midg,igrid,midg -1.3189193E-10 3.3336677E-11 1,midg,midg; igrid,midg,midg -1.3798000E-10 1.1238816E-10 gauss-seidel spectral radius is 0.9817860 estimated iterations to convergence 61 setup time was (sec) 0.4600000 now iterating at: 09:25:38 rms-change max change #iterations 5.8031492E-02 12.50918 at 10iterations 3.5178531E-03 0.6726274 at 20iterations 2.1187439E-04 3.7357330E-02 at 30iterations 1.3259050E-05 2.7427673E-03 at 40iterations 8.4030535E-07 1.9836426E-04 at 50iterations finished qdiffx linear iterations at : 09:25:40 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 8.4030535E-07 1.9836426E-04 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 09:25:41 3.269u 0.191s 0:03.73 92.4% 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 Mon Oct 10 2011 at 09:25:41 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: 235 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2229 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: 1.597869 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): -19.91700 46.92200 ymin,ymax (A): -19.54700 25.38200 zmin,zma (A): -18.14600 38.10800 x,y,z range (A): 66.83900 44.92900 56.25400 scale (grids/A): 1.597869 object centre (A): 13.50250 2.917500 9.981001 number of atom coordinates read : 2229 total number of charged atoms : 2093 net assigned charge : -0.9999955 assigned positive charge : 334.8683 centred at (gu) : 92.54634 88.67509 82.89491 assigned negative charge : -335.8689 centred at (gu) : 92.41549 88.59747 83.00710 start vw surface at 0.1500000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 46084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21932 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 13312 mr = 29284 m= 1253 mr = 9022 m= 33 mr = 597 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 339 time to turn everything in is 0.3700000 number of dielectric boundary points 21779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 303 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15906 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) : 0.5326231 object centre at (A) : 13.50250 2.917500 9.981001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8118135E-03 4.1465208E-04 midg,1,midg; midg,igrid,midg -3.3293895E-03 -2.8084184E-03 1,midg,midg; igrid,midg,midg -2.6716664E-03 -7.2095112E-04 gauss-seidel spectral radius is 0.9980068 estimated iterations to convergence 178 setup time was (sec) 0.6400000 now iterating at: 09:25:42 rms-change max change #iterations 2.698276 132.0638 at 10iterations 1.075552 50.31431 at 20iterations 0.4284565 18.38528 at 30iterations 0.1711105 7.981586 at 40iterations 6.8004802E-02 3.013749 at 50iterations 2.7248908E-02 1.128002 at 60iterations 1.0825040E-02 0.4490051 at 70iterations 4.3320591E-03 0.2123032 at 80iterations 1.7289399E-03 7.2469711E-02 at 90iterations 6.9130969E-04 2.9289246E-02 at 100iterations 2.7553999E-04 1.2615442E-02 at 110iterations 1.1029344E-04 5.2208900E-03 at 120iterations finished qdiffx linear iterations at : 09:25:48 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 1.1029344E-04 5.2208900E-03 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 09:25:49 7.185u 0.229s 0:07.86 94.1% 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 09:25:49 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: 235 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2229 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.396804 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): -19.91700 46.92200 ymin,ymax (A): -19.54700 25.38200 zmin,zma (A): -18.14600 38.10800 x,y,z range (A): 66.83900 44.92900 56.25400 scale (grids/A): 2.396804 object centre (A): 13.50250 2.917500 9.981001 number of atom coordinates read : 2229 total number of charged atoms : 2093 net assigned charge : -0.9999955 assigned positive charge : 334.8683 centred at (gu) : 93.81944 88.01238 79.34251 assigned negative charge : -335.8689 centred at (gu) : 93.62315 87.89613 79.51056 start vw surface at 0.1200000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 106722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21932 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 46413 mr = 71767 m= 12838 mr = 36064 m= 1925 mr = 9738 m= 148 mr = 1223 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1109 time to turn everything in is 0.7800000 number of dielectric boundary points 49184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 16705 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) : 1.597869 object centre at (A) : 13.50250 2.917500 9.981001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9870850E-02 -9.3862722E-03 midg,1,midg; midg,igrid,midg -4.6133261E-02 -3.2102071E-02 1,midg,midg; igrid,midg,midg -7.6008059E-02 -1.5717165E-03 gauss-seidel spectral radius is 0.9990462 estimated iterations to convergence 256 setup time was (sec) 1.070000 now iterating at: 09:25:50 rms-change max change #iterations 7.036658 279.0551 at 10iterations 3.791705 103.2924 at 20iterations 2.042000 54.17977 at 30iterations 1.092868 26.36374 at 40iterations 0.5834224 15.19528 at 50iterations 0.3096810 8.419244 at 60iterations 0.1645600 4.057182 at 70iterations 8.7564923E-02 2.154872 at 80iterations 4.6617940E-02 1.183029 at 90iterations 2.4785819E-02 0.6211700 at 100iterations 1.3154205E-02 0.3277128 at 110iterations 6.9840993E-03 0.1765709 at 120iterations 3.7156062E-03 9.4263077E-02 at 130iterations 1.9727217E-03 4.5039177E-02 at 140iterations 1.0468380E-03 2.6733160E-02 at 150iterations 5.5533735E-04 1.4080048E-02 at 160iterations 2.9546552E-04 7.1163177E-03 at 170iterations 1.5684935E-04 3.9043427E-03 at 180iterations finished qdiffx linear iterations at : 09:26:01 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 1.5684935E-04 3.9043427E-03 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 09:26:02 12.468u 0.258s 0:13.03 97.5% 0+0k 0+0io 0pf+0w