Tue Oct 11 03:22:57 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 Tue Oct 11 2011 at 03:22:57 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1167 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7355067 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): -6.374000 30.50400 ymin,ymax (A): 1.321000 39.65300 zmin,zma (A): -2.365000 46.03700 x,y,z range (A): 36.87800 38.33200 48.40200 scale (grids/A): 0.7355067 object centre (A): 12.06500 20.48700 21.83600 number of atom coordinates read : 1167 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 89.05431 89.29846 88.65116 assigned negative charge : -169.8232 centred at (gu) : 88.73068 89.28297 88.66991 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4333 nv = 96 ne = 84 npr = 22460 no. pairs analyzed = 22460 no. exposed pairs = 1474 no. arc points = 11065 no. surface atoms = 499 nbur = 668 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 272 mr = 2238 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.1200000 number of dielectric boundary points 2322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 908 ## 72 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4434 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2651081E-07 6.3141613E-08 midg,1,midg; midg,igrid,midg 9.3044143E-08 8.5506898E-08 1,midg,midg; igrid,midg,midg -9.0217021E-08 2.0371293E-07 gauss-seidel spectral radius is 0.9902728 estimated iterations to convergence 82 setup time was (sec) 0.3200000 now iterating at: 03:22:57 rms-change max change #iterations 0.1691644 30.30639 at 10iterations 2.2483865E-02 3.555332 at 20iterations 2.9160148E-03 0.5259972 at 30iterations 3.7511659E-04 6.9290161E-02 at 40iterations 4.9646878E-05 8.4257126E-03 at 50iterations finished qdiffx linear iterations at : 03:23:00 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.9646878E-05 8.4257126E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 03:23:01 3.354u 0.181s 0:03.95 89.3% 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 Tue Oct 11 2011 at 03:23:01 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1167 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.206520 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): -6.374000 30.50400 ymin,ymax (A): 1.321000 39.65300 zmin,zma (A): -2.365000 46.03700 x,y,z range (A): 36.87800 38.33200 48.40200 scale (grids/A): 2.206520 object centre (A): 12.06500 20.48700 21.83600 number of atom coordinates read : 1167 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 87.16299 87.89543 85.95360 assigned negative charge : -169.8232 centred at (gu) : 86.19225 87.84905 86.00989 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 45107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11065 grid for indexing accessible points = 1.400000 m= 17045 mr = 29375 m= 3389 mr = 12683 m= 330 mr = 2275 m= 4 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1477 time to turn everything in is 0.2500000 number of dielectric boundary points 21373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8445 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) : 0.7355067 object centre at (A) : 12.06500 20.48700 21.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2532072E-02 3.2319163E-03 midg,1,midg; midg,igrid,midg 3.8028352E-02 3.2392688E-02 1,midg,midg; igrid,midg,midg -2.6986375E-02 4.0792122E-02 gauss-seidel spectral radius is 0.9988242 estimated iterations to convergence 231 setup time was (sec) 0.4700000 now iterating at: 03:23:01 rms-change max change #iterations 3.557742 212.3416 at 10iterations 1.753319 84.90131 at 20iterations 0.8624770 36.08855 at 30iterations 0.4262946 16.65719 at 40iterations 0.2107849 7.317980 at 50iterations 0.1039643 4.057858 at 60iterations 5.1198300E-02 1.981953 at 70iterations 2.5220457E-02 0.9401073 at 80iterations 1.2420884E-02 0.4336274 at 90iterations 6.1301766E-03 0.2416449 at 100iterations 3.0234996E-03 0.1116638 at 110iterations 1.4937180E-03 5.5065155E-02 at 120iterations finished qdiffx linear iterations at : 03:23:08 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 1.4937180E-03 5.5065155E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 03:23:09 7.649u 0.223s 0:08.17 96.2% 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 Tue Oct 11 2011 at 03:23:09 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1167 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.309780 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): -6.374000 30.50400 ymin,ymax (A): 1.321000 39.65300 zmin,zma (A): -2.365000 46.03700 x,y,z range (A): 36.87800 38.33200 48.40200 scale (grids/A): 3.309780 object centre (A): 12.06500 20.48700 21.83600 number of atom coordinates read : 1167 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 85.74454 86.84312 83.93045 assigned negative charge : -169.8232 centred at (gu) : 84.28831 86.77359 84.01487 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 103730 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11065 grid for indexing accessible points = 1.400000 m= 52081 mr = 70915 m= 21716 mr = 42536 m= 6397 mr = 17812 m= 1323 mr = 4956 m= 145 mr = 1019 m= 4 mr = 95 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 4657 time to turn everything in is 0.7000000 number of dielectric boundary points 48064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 8488 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) : 2.206520 object centre at (A) : 12.06500 20.48700 21.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1351450 -2.7575879E-03 midg,1,midg; midg,igrid,midg 0.3306738 0.2716755 1,midg,midg; igrid,midg,midg -0.2148238 0.2965333 gauss-seidel spectral radius is 0.9992889 estimated iterations to convergence 296 setup time was (sec) 0.9400000 now iterating at: 03:23:10 rms-change max change #iterations 7.763225 314.5240 at 10iterations 4.507459 114.1045 at 20iterations 2.603334 56.73331 at 30iterations 1.509025 34.44106 at 40iterations 0.8707981 19.92401 at 50iterations 0.5035843 11.06806 at 60iterations 0.2918858 6.435029 at 70iterations 0.1685676 3.513653 at 80iterations 9.7691789E-02 2.042419 at 90iterations 5.6408245E-02 1.289238 at 100iterations 3.2639883E-02 0.7387066 at 110iterations 1.8954679E-02 0.4039459 at 120iterations 1.0917368E-02 0.2308416 at 130iterations 6.3325753E-03 0.1439209 at 140iterations 3.6651341E-03 7.7882767E-02 at 150iterations 2.1225908E-03 4.7378540E-02 at 160iterations 1.2313497E-03 2.7040362E-02 at 170iterations 7.1237382E-04 1.5477419E-02 at 180iterations finished qdiffx linear iterations at : 03:23:21 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 7.1237382E-04 1.5477419E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 03:23:22 11.996u 0.236s 0:12.64 96.6% 0+0k 0+0io 0pf+0w