Sat Oct 8 14:33:19 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 14:33:19 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 = 3040 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 0.6404606 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): -12.16200 43.42300 ymin,ymax (A): -22.80600 22.45200 zmin,zma (A): -7.571000 47.93800 x,y,z range (A): 55.58500 45.25800 55.50900 scale (grids/A): 0.6404606 object centre (A): 15.63050 -0.1770000 20.18350 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : -0.9999923 assigned positive charge : 455.0816 centred at (gu) : 88.80405 89.77982 91.54504 assigned negative charge : -456.0822 centred at (gu) : 88.78564 89.67705 91.47398 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8219 nv = 96 ne = 84 npr = 63529 no. pairs analyzed = 63529 no. exposed pairs = 3444 no. arc points = 24467 no. surface atoms = 1170 nbur = 1870 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 408 mr = 4771 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.4100000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2376 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10048 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.2272082E-09 1.1549881E-08 midg,1,midg; midg,igrid,midg -1.6711668E-08 1.1905088E-08 1,midg,midg; igrid,midg,midg -5.3173212E-09 7.4076084E-10 gauss-seidel spectral radius is 0.9874027 estimated iterations to convergence 73 setup time was (sec) 0.6800000 now iterating at: 14:33:20 rms-change max change #iterations 0.1552124 22.91738 at 10iterations 1.5402477E-02 2.190720 at 20iterations 1.5393236E-03 0.2097931 at 30iterations 1.5832460E-04 2.3228645E-02 at 40iterations 1.6771970E-05 2.0484924E-03 at 50iterations finished qdiffx linear iterations at : 14:33:23 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.6771970E-05 2.0484924E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:33:24 4.247u 0.266s 0:04.89 92.0% 0+0k 0+0io 6pf+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 14:33:24 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 = 3040 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 1.921382 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): -12.16200 43.42300 ymin,ymax (A): -22.80600 22.45200 zmin,zma (A): -7.571000 47.93800 x,y,z range (A): 55.58500 45.25800 55.50900 scale (grids/A): 1.921382 object centre (A): 15.63050 -0.1770000 20.18350 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : -0.9999923 assigned positive charge : 455.0816 centred at (gu) : 86.41136 89.33859 94.63493 assigned negative charge : -456.0822 centred at (gu) : 86.35667 89.03084 94.42159 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 90271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24467 grid for indexing accessible points = 1.400000 m= 32476 mr = 65184 m= 4637 mr = 24419 m= 262 mr = 2745 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 492 time to turn everything in is 0.7700000 number of dielectric boundary points 35209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 22805 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) : 0.6404606 object centre at (A) : 15.63050 -0.1770000 20.18350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3856568E-02 1.6034028E-02 midg,1,midg; midg,igrid,midg -8.3015254E-03 1.7772717E-02 1,midg,midg; igrid,midg,midg -4.0047191E-02 1.3517478E-02 gauss-seidel spectral radius is 0.9986947 estimated iterations to convergence 219 setup time was (sec) 1.090000 now iterating at: 14:33:25 rms-change max change #iterations 4.742428 207.1571 at 10iterations 2.262419 75.27628 at 20iterations 1.078849 33.32277 at 30iterations 0.5154611 14.64725 at 40iterations 0.2459199 7.132373 at 50iterations 0.1174273 3.503969 at 60iterations 5.6047238E-02 1.873296 at 70iterations 2.6753338E-02 0.7484550 at 80iterations 1.2754903E-02 0.3552246 at 90iterations 6.0786754E-03 0.1867905 at 100iterations 2.9054433E-03 8.0019951E-02 at 110iterations 1.3869285E-03 4.1012764E-02 at 120iterations finished qdiffx linear iterations at : 14:33:34 total time elapsed so far: 9.850000 # loops : 120 mean,max change (kT/e) : 1.3869285E-03 4.1012764E-02 energy calculations done at 9.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.03000 DelPhi exited at 14:33:34 10.035u 0.326s 0:10.72 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 Sat Oct 8 2011 at 14:33:34 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 2.882072 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): -12.16200 43.42300 ymin,ymax (A): -22.80600 22.45200 zmin,zma (A): -7.571000 47.93800 x,y,z range (A): 55.58500 45.25800 55.50900 scale (grids/A): 2.882072 object centre (A): 15.63050 -0.1770000 20.18350 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : -0.9999923 assigned positive charge : 455.0816 centred at (gu) : 84.61691 89.00784 96.95205 assigned negative charge : -456.0822 centred at (gu) : 84.53506 88.54620 96.63244 start vw surface at 0.1800000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 209399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24467 grid for indexing accessible points = 1.400000 m= 106741 mr = 157705 m= 36907 mr = 88912 m= 8273 mr = 29752 m= 1162 mr = 5973 m= 72 mr = 785 m= 0 mr = 26 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 1548 time to turn everything in is 2.040000 number of dielectric boundary points 79401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 23139 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) : 1.921382 object centre at (A) : 15.63050 -0.1770000 20.18350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5987292E-02 0.2396478 midg,1,midg; midg,igrid,midg -6.5729000E-02 0.2089749 1,midg,midg; igrid,midg,midg -0.6058870 0.1883126 gauss-seidel spectral radius is 0.9992782 estimated iterations to convergence 294 setup time was (sec) 2.370000 now iterating at: 14:33:37 rms-change max change #iterations 10.98678 405.9428 at 10iterations 6.467033 141.0562 at 20iterations 3.771110 81.65286 at 30iterations 2.203094 44.34757 at 40iterations 1.279965 22.19460 at 50iterations 0.7438552 14.14035 at 60iterations 0.4326063 7.899446 at 70iterations 0.2508688 4.465173 at 80iterations 0.1455665 2.631050 at 90iterations 8.4258839E-02 1.714273 at 100iterations 4.8756994E-02 0.7492952 at 110iterations 2.8287984E-02 0.4730511 at 120iterations 1.6371699E-02 0.2761627 at 130iterations 9.4907209E-03 0.1624889 at 140iterations 5.4870341E-03 9.2245102E-02 at 150iterations 3.1852170E-03 5.2988052E-02 at 160iterations 1.8408409E-03 3.1565189E-02 at 170iterations 1.0665281E-03 1.7406464E-02 at 180iterations finished qdiffx linear iterations at : 14:33:52 total time elapsed so far: 16.93000 # loops : 180 mean,max change (kT/e) : 1.0665281E-03 1.7406464E-02 energy calculations done at 16.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.11000 DelPhi exited at 14:33:52 17.114u 0.342s 0:17.74 98.3% 0+0k 0+0io 0pf+0w