Tue Oct 11 08:21:59 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 08:21:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3111 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: 0.5771164 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 0.5771164 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3111 total number of charged atoms : 2973 net assigned charge : -5.999976 assigned positive charge : 461.6750 centred at (gu) : 90.99263 89.31594 89.92919 assigned negative charge : -467.6760 centred at (gu) : 90.96671 89.28848 89.97624 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6757 nv = 96 ne = 84 npr = 63874 no. pairs analyzed = 63874 no. exposed pairs = 3959 no. arc points = 27291 no. surface atoms = 1331 nbur = 1780 mkacc time = 0.1700000 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 = 1.484000 m= 316 mr = 3577 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2854 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8730 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0521899E-10 -2.1451541E-09 midg,1,midg; midg,igrid,midg -2.0698661E-09 -5.2703458E-10 1,midg,midg; igrid,midg,midg -1.3789579E-09 -7.9909257E-10 gauss-seidel spectral radius is 0.9845146 estimated iterations to convergence 66 setup time was (sec) 0.6200000 now iterating at: 08:22:00 rms-change max change #iterations 9.9283978E-02 16.02007 at 10iterations 7.7476995E-03 1.248522 at 20iterations 8.6395029E-04 0.1337186 at 30iterations 2.2310599E-04 3.2849312E-02 at 40iterations 7.5896081E-05 1.1445999E-02 at 50iterations finished qdiffx linear iterations at : 08:22:05 total time elapsed so far: 4.820000 # loops : 50 mean,max change (kT/e) : 7.5896081E-05 1.1445999E-02 energy calculations done at 4.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.990000 DelPhi exited at 08:22:05 4.996u 0.447s 0:05.74 94.5% 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 Tue Oct 11 2011 at 08:22:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3111 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: 1.731349 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 1.731349 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3111 total number of charged atoms : 2973 net assigned charge : -5.999976 assigned positive charge : 461.6750 centred at (gu) : 92.97746 87.94727 89.78671 assigned negative charge : -467.6760 centred at (gu) : 92.89973 87.86517 89.92872 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 74117 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27291 grid for indexing accessible points = 1.400000 m= 25082 mr = 50658 m= 3223 mr = 17700 m= 114 mr = 1743 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1323 time to turn everything in is 0.6500000 number of dielectric boundary points 32418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 23058 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) : 0.5771164 object centre at (A) : 123.1420 13.69150 36.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5770448E-02 -3.3129513E-02 midg,1,midg; midg,igrid,midg -8.3900439E-03 3.0038124E-03 1,midg,midg; igrid,midg,midg -9.5815230E-03 3.8161308E-03 gauss-seidel spectral radius is 0.9984062 estimated iterations to convergence 199 setup time was (sec) 1.030000 now iterating at: 08:22:07 rms-change max change #iterations 3.855614 179.0596 at 10iterations 1.695574 60.13894 at 20iterations 0.7434955 25.29144 at 30iterations 0.3285764 11.89698 at 40iterations 0.1446993 4.602445 at 50iterations 6.3905716E-02 2.379210 at 60iterations 2.8118849E-02 0.9695320 at 70iterations 1.2434729E-02 0.4092178 at 80iterations 5.5467277E-03 0.1947198 at 90iterations 2.5236716E-03 8.8381171E-02 at 100iterations 1.1938910E-03 5.3184509E-02 at 110iterations 5.9822854E-04 2.1775961E-02 at 120iterations finished qdiffx linear iterations at : 08:22:17 total time elapsed so far: 11.50000 # loops : 120 mean,max change (kT/e) : 5.9822854E-04 2.1775961E-02 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.66000 DelPhi exited at 08:22:18 11.664u 0.502s 0:12.77 95.2% 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 08:22:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3111 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: 2.597024 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 2.597024 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3111 total number of charged atoms : 2973 net assigned charge : -5.999976 assigned positive charge : 461.6750 centred at (gu) : 94.46591 86.92062 89.67967 assigned negative charge : -467.6760 centred at (gu) : 94.34939 86.79754 89.89287 start vw surface at 0.1400000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 171447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27291 grid for indexing accessible points = 1.400000 m= 83606 mr = 123298 m= 27256 mr = 66904 m= 5392 mr = 21008 m= 503 mr = 3727 m= 7 mr = 243 m= 0 mr = 2 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 4770 time to turn everything in is 1.630000 number of dielectric boundary points 73029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 23773 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) : 1.731349 object centre at (A) : 123.1420 13.69150 36.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3446772 -0.3773286 midg,1,midg; midg,igrid,midg 5.8123432E-02 2.2886412E-02 1,midg,midg; igrid,midg,midg -0.1880902 0.1313944 gauss-seidel spectral radius is 0.9992086 estimated iterations to convergence 281 setup time was (sec) 1.980000 now iterating at: 08:22:21 rms-change max change #iterations 9.560390 294.1331 at 10iterations 5.558336 140.6012 at 20iterations 3.184843 68.95517 at 30iterations 1.827432 37.30638 at 40iterations 1.039218 21.77250 at 50iterations 0.5905669 12.33111 at 60iterations 0.3361343 6.745239 at 70iterations 0.1903858 3.940632 at 80iterations 0.1076791 2.102933 at 90iterations 6.1035998E-02 1.319316 at 100iterations 3.4585778E-02 0.7151966 at 110iterations 1.9493507E-02 0.4044075 at 120iterations 1.1085155E-02 0.2221146 at 130iterations 6.2940046E-03 0.1162052 at 140iterations 3.5889368E-03 6.9172859E-02 at 150iterations 2.0709238E-03 4.3833733E-02 at 160iterations 1.2182534E-03 2.4396420E-02 at 170iterations 7.4037520E-04 1.4450073E-02 at 180iterations finished qdiffx linear iterations at : 08:22:39 total time elapsed so far: 19.91000 # loops : 180 mean,max change (kT/e) : 7.4037520E-04 1.4450073E-02 energy calculations done at 19.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.07000 DelPhi exited at 08:22:39 20.072u 0.520s 0:21.30 96.6% 0+0k 0+0io 0pf+0w