Sat Oct 8 13:54:29 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 Sat Oct 8 2011 at 13:54:29 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6407949 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): -12.40600 43.15000 ymin,ymax (A): -22.49700 22.40400 zmin,zma (A): -7.351000 47.19900 x,y,z range (A): 55.55600 44.90100 54.55000 scale (grids/A): 0.6407949 object centre (A): 15.37200 -4.6500206E-02 19.92400 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8235 centred at (gu) : 88.77556 89.48869 91.71257 assigned negative charge : -455.8243 centred at (gu) : 88.77348 89.39875 91.61561 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8235 nv = 96 ne = 84 npr = 64021 no. pairs analyzed = 64021 no. exposed pairs = 3454 no. arc points = 24028 no. surface atoms = 1181 nbur = 1862 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4799 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2329 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10062 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.5526023E-09 1.9245270E-08 midg,1,midg; midg,igrid,midg -1.4346823E-08 1.0952452E-08 1,midg,midg; igrid,midg,midg -6.0421246E-10 9.1136730E-11 gauss-seidel spectral radius is 0.9874137 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 13:54:30 rms-change max change #iterations 0.1599529 24.58402 at 10iterations 1.6446192E-02 2.175285 at 20iterations 1.6874684E-03 0.1951561 at 30iterations 1.9216200E-04 2.5382996E-02 at 40iterations 2.5343223E-05 3.0288696E-03 at 50iterations finished qdiffx linear iterations at : 13:54:34 total time elapsed so far: 5.070000 # loops : 50 mean,max change (kT/e) : 2.5343223E-05 3.0288696E-03 energy calculations done at 5.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 13:54:35 5.244u 0.478s 0:05.98 95.4% 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 Sat Oct 8 2011 at 13:54:35 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.922385 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): -12.40600 43.15000 ymin,ymax (A): -22.49700 22.40400 zmin,zma (A): -7.351000 47.19900 x,y,z range (A): 55.55600 44.90100 54.55000 scale (grids/A): 1.922385 object centre (A): 15.37200 -4.6500206E-02 19.92400 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8235 centred at (gu) : 86.32626 88.46535 95.13734 assigned negative charge : -455.8243 centred at (gu) : 86.32028 88.19612 94.84685 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89491 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24028 grid for indexing accessible points = 1.400000 m= 32506 mr = 64670 m= 4896 mr = 24473 m= 300 mr = 3027 m= 5 mr = 92 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 270 time to turn everything in is 0.7300000 number of dielectric boundary points 34937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 22820 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) : 0.6407949 object centre at (A) : 15.37200 -4.6500206E-02 19.92400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9827239E-02 2.1963887E-02 midg,1,midg; midg,igrid,midg -1.6062717E-03 2.0522220E-02 1,midg,midg; igrid,midg,midg -3.5577558E-02 1.0103856E-02 gauss-seidel spectral radius is 0.9986927 estimated iterations to convergence 219 setup time was (sec) 1.090000 now iterating at: 13:54:36 rms-change max change #iterations 4.767569 171.7716 at 10iterations 2.279078 67.00851 at 20iterations 1.084645 34.23465 at 30iterations 0.5172893 15.79953 at 40iterations 0.2468225 7.112600 at 50iterations 0.1176602 3.484150 at 60iterations 5.6249384E-02 1.709503 at 70iterations 2.6880922E-02 0.7669687 at 80iterations 1.2761419E-02 0.3497674 at 90iterations 6.1122323E-03 0.1715517 at 100iterations 2.9202034E-03 8.3227158E-02 at 110iterations 1.3940876E-03 4.0086746E-02 at 120iterations finished qdiffx linear iterations at : 13:54:48 total time elapsed so far: 12.56000 # loops : 120 mean,max change (kT/e) : 1.3940876E-03 4.0086746E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 13:54:48 12.739u 0.537s 0:13.55 97.8% 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 13:54:48 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.883577 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): -12.40600 43.15000 ymin,ymax (A): -22.49700 22.40400 zmin,zma (A): -7.351000 47.19900 x,y,z range (A): 55.55600 44.90100 54.55000 scale (grids/A): 2.883577 object centre (A): 15.37200 -4.6500206E-02 19.92400 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8235 centred at (gu) : 84.48928 87.69798 97.70560 assigned negative charge : -455.8243 centred at (gu) : 84.48032 87.29418 97.27016 start vw surface at 0.1200000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 207482 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24028 grid for indexing accessible points = 1.400000 m= 106434 mr = 156241 m= 37596 mr = 88684 m= 8635 mr = 30458 m= 1221 mr = 6364 m= 64 mr = 777 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 982 time to turn everything in is 1.950000 number of dielectric boundary points 78892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 23168 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) : 1.922385 object centre at (A) : 15.37200 -4.6500206E-02 19.92400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7009949E-02 0.3450246 midg,1,midg; midg,igrid,midg -2.3366436E-03 0.2477873 1,midg,midg; igrid,midg,midg -0.5954023 0.1530420 gauss-seidel spectral radius is 0.9992775 estimated iterations to convergence 294 setup time was (sec) 2.340000 now iterating at: 13:54:51 rms-change max change #iterations 11.02204 498.0966 at 10iterations 6.457855 130.8787 at 20iterations 3.773640 78.57994 at 30iterations 2.202219 44.96168 at 40iterations 1.278705 24.27105 at 50iterations 0.7442006 13.22532 at 60iterations 0.4324113 7.751948 at 70iterations 0.2505841 4.440114 at 80iterations 0.1454642 2.597586 at 90iterations 8.4278412E-02 1.489386 at 100iterations 4.8878849E-02 0.7882891 at 110iterations 2.8270964E-02 0.4598255 at 120iterations 1.6400283E-02 0.2634993 at 130iterations 9.5166592E-03 0.1611280 at 140iterations 5.5212290E-03 9.4848633E-02 at 150iterations 3.2080635E-03 5.5816650E-02 at 160iterations 1.8738927E-03 2.9481411E-02 at 170iterations 1.0974525E-03 1.7919540E-02 at 180iterations finished qdiffx linear iterations at : 13:55:10 total time elapsed so far: 21.64000 # loops : 180 mean,max change (kT/e) : 1.0974525E-03 1.7919540E-02 energy calculations done at 21.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.80000 DelPhi exited at 13:55:11 21.808u 0.580s 0:22.65 98.8% 0+0k 0+0io 0pf+0w