Sun Oct 9 15:59:41 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 15:59:41 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5657 !!! WARNING: GLM 113 has a net charge of -0.0940 !!! WARNING: HIR 669 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4864385 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): 66.87800 138.0990 ymin,ymax (A): -11.99500 56.59600 zmin,zma (A): -3.191000 69.99400 x,y,z range (A): 71.22100 68.59100 73.18501 scale (grids/A): 0.4864385 object centre (A): 102.4885 22.30050 33.40150 number of atom coordinates read : 5657 total number of charged atoms : 5479 net assigned charge : -3.579955 assigned positive charge : 871.2902 centred at (gu) : 89.02744 90.66290 90.09589 assigned negative charge : -874.8779 centred at (gu) : 89.04888 90.62344 90.12304 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8154 nv = 96 ne = 84 npr = 114726 no. pairs analyzed = 114726 no. exposed pairs = 6588 no. arc points = 45834 no. surface atoms = 2219 nbur = 3438 mkacc time = 0.2600000 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 = 1.764000 m= 248 mr = 4383 m= 0 mr = 1 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.5200000 number of dielectric boundary points 4018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4352 ## 765 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11127 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1766897E-11 -4.7450141E-11 midg,1,midg; midg,igrid,midg -4.9615607E-11 3.0519004E-11 1,midg,midg; igrid,midg,midg 8.1596075E-12 -3.0691481E-11 gauss-seidel spectral radius is 0.9784486 estimated iterations to convergence 56 setup time was (sec) 0.7200000 now iterating at: 15:59:42 rms-change max change #iterations 5.6542173E-02 9.232903 at 10iterations 4.9990057E-03 0.9136353 at 20iterations 1.4798441E-03 0.2898293 at 30iterations 5.1327684E-04 0.1016235 at 40iterations 1.7860912E-04 3.5438538E-02 at 50iterations finished qdiffx linear iterations at : 15:59:44 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.7860912E-04 3.5438538E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 15:59:45 3.345u 0.153s 0:03.79 92.0% 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 15:59:45 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5657 !!! WARNING: GLM 113 has a net charge of -0.0940 !!! WARNING: HIR 669 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.459315 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): 66.87800 138.0990 ymin,ymax (A): -11.99500 56.59600 zmin,zma (A): -3.191000 69.99400 x,y,z range (A): 71.22100 68.59100 73.18501 scale (grids/A): 1.459315 object centre (A): 102.4885 22.30050 33.40150 number of atom coordinates read : 5657 total number of charged atoms : 5479 net assigned charge : -3.579955 assigned positive charge : 871.2902 centred at (gu) : 87.08003 91.98684 90.28580 assigned negative charge : -874.8779 centred at (gu) : 87.14631 91.87029 90.36891 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 94303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45834 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26123 mr = 66211 m= 1981 mr = 17703 m= 35 mr = 823 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2799 time to turn everything in is 0.6600000 number of dielectric boundary points 37705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 702 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 40342 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) : 0.4864385 object centre at (A) : 102.4885 22.30050 33.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1331624E-04 5.4386291E-03 midg,1,midg; midg,igrid,midg -5.2953796E-03 1.0509357E-02 1,midg,midg; igrid,midg,midg -2.5942503E-02 -1.7061289E-03 gauss-seidel spectral radius is 0.9979576 estimated iterations to convergence 176 setup time was (sec) 0.9300000 now iterating at: 15:59:46 rms-change max change #iterations 3.739597 155.8957 at 10iterations 1.483729 53.81085 at 20iterations 0.5879217 18.78906 at 30iterations 0.2327347 7.408720 at 40iterations 9.2859313E-02 2.799136 at 50iterations 3.6916994E-02 1.155791 at 60iterations 1.4933990E-02 0.4716501 at 70iterations 6.1677801E-03 0.2058334 at 80iterations 2.7515932E-03 0.1026802 at 90iterations 1.3702016E-03 5.5137634E-02 at 100iterations 7.8322319E-04 3.2642365E-02 at 110iterations 4.9390446E-04 1.9287109E-02 at 120iterations finished qdiffx linear iterations at : 15:59:52 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 4.9390446E-04 1.9287109E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 15:59:53 7.131u 0.169s 0:07.68 94.9% 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 15:59:53 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5657 !!! WARNING: GLM 113 has a net charge of -0.0940 !!! WARNING: HIR 669 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.188973 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): 66.87800 138.0990 ymin,ymax (A): -11.99500 56.59600 zmin,zma (A): -3.191000 69.99400 x,y,z range (A): 71.22100 68.59100 73.18501 scale (grids/A): 2.188973 object centre (A): 102.4885 22.30050 33.40150 number of atom coordinates read : 5657 total number of charged atoms : 5479 net assigned charge : -3.579955 assigned positive charge : 871.2902 centred at (gu) : 85.61929 92.97994 90.42843 assigned negative charge : -874.8779 centred at (gu) : 85.71947 92.80540 90.55337 start vw surface at 0.2000000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 220936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45834 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 96179 mr = 163538 m= 22384 mr = 75867 m= 2600 mr = 16225 m= 90 mr = 1477 m= 0 mr = 15 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 9354 time to turn everything in is 1.510000 number of dielectric boundary points 85067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 43618 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) : 1.459315 object centre at (A) : 102.4885 22.30050 33.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2845034E-02 0.2906781 midg,1,midg; midg,igrid,midg -0.1195066 0.2982803 1,midg,midg; igrid,midg,midg -0.7345505 6.9377325E-02 gauss-seidel spectral radius is 0.9991243 estimated iterations to convergence 267 setup time was (sec) 1.810000 now iterating at: 15:59:55 rms-change max change #iterations 10.44826 258.3354 at 10iterations 5.842297 179.3563 at 20iterations 3.265955 74.92963 at 30iterations 1.812171 37.11265 at 40iterations 1.003204 21.50057 at 50iterations 0.5532979 11.04860 at 60iterations 0.3045570 6.610029 at 70iterations 0.1673282 3.407520 at 80iterations 9.1960452E-02 1.772821 at 90iterations 5.0535873E-02 0.8917809 at 100iterations 2.7786940E-02 0.6132140 at 110iterations 1.5242891E-02 0.2717972 at 120iterations 8.4101381E-03 0.1566696 at 130iterations 4.6458594E-03 8.7560654E-02 at 140iterations 2.5786858E-03 4.9336135E-02 at 150iterations 1.4577053E-03 3.0338287E-02 at 160iterations 8.4282993E-04 1.8236160E-02 at 170iterations 5.0523860E-04 1.0963440E-02 at 180iterations finished qdiffx linear iterations at : 16:00:05 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 5.0523860E-04 1.0963440E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 16:00:05 12.023u 0.197s 0:12.57 97.1% 0+0k 0+0io 0pf+0w