Sat Oct 15 15:07:09 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 15 2011 at 15:07:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2851 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6287864 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): -12.16400 36.64400 ymin,ymax (A): 3.357000 51.96000 zmin,zma (A): -11.14900 45.46800 x,y,z range (A): 48.80800 48.60300 56.61700 scale (grids/A): 0.6287864 object centre (A): 12.24000 27.65850 17.15950 number of atom coordinates read : 2851 total number of charged atoms : 2704 net assigned charge : 3.500020 assigned positive charge : 431.9825 centred at (gu) : 90.31124 90.73123 91.78348 assigned negative charge : -428.4832 centred at (gu) : 90.09694 90.61481 91.72913 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7516 nv = 96 ne = 84 npr = 57592 no. pairs analyzed = 57592 no. exposed pairs = 3467 no. arc points = 23797 no. surface atoms = 1174 nbur = 1677 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 4273 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2401 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9104 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1080785E-09 1.2575008E-08 midg,1,midg; midg,igrid,midg -6.4941856E-09 1.6715372E-08 1,midg,midg; igrid,midg,midg -1.6054656E-08 2.4749127E-08 gauss-seidel spectral radius is 0.9869165 estimated iterations to convergence 72 setup time was (sec) 0.4500000 now iterating at: 15:07:10 rms-change max change #iterations 0.1397198 17.99965 at 10iterations 1.3736400E-02 2.086459 at 20iterations 1.3529167E-03 0.2236824 at 30iterations 1.5886246E-04 2.4923325E-02 at 40iterations 3.3913318E-05 6.4582825E-03 at 50iterations finished qdiffx linear iterations at : 15:07:13 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 3.3913318E-05 6.4582825E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 15:07:13 3.914u 0.223s 0:04.43 93.2% 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 Sat Oct 15 2011 at 15:07:13 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 = 2851 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.886359 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): -12.16400 36.64400 ymin,ymax (A): 3.357000 51.96000 zmin,zma (A): -11.14900 45.46800 x,y,z range (A): 48.80800 48.60300 56.61700 scale (grids/A): 1.886359 object centre (A): 12.24000 27.65850 17.15950 number of atom coordinates read : 2851 total number of charged atoms : 2704 net assigned charge : 3.500020 assigned positive charge : 431.9825 centred at (gu) : 90.93295 92.19270 95.35000 assigned negative charge : -428.4832 centred at (gu) : 90.29054 91.84393 95.18711 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23797 grid for indexing accessible points = 1.400000 m= 29451 mr = 57295 m= 4294 mr = 21919 m= 218 mr = 2478 m= 5 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.4100000 number of dielectric boundary points 33162 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 21200 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) : 0.6287864 object centre at (A) : 12.24000 27.65850 17.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5664641E-02 1.2766527E-02 midg,1,midg; midg,igrid,midg -1.2584494E-02 8.0522662E-04 1,midg,midg; igrid,midg,midg -6.8591721E-03 5.3349797E-02 gauss-seidel spectral radius is 0.9986324 estimated iterations to convergence 214 setup time was (sec) 0.7000000 now iterating at: 15:07:14 rms-change max change #iterations 4.416896 179.8473 at 10iterations 2.063925 74.85944 at 20iterations 0.9712381 31.64493 at 30iterations 0.4551998 14.12679 at 40iterations 0.2137986 8.270196 at 50iterations 0.1003788 3.022751 at 60iterations 4.6999365E-02 1.619862 at 70iterations 2.2058606E-02 0.6791782 at 80iterations 1.0369408E-02 0.3098326 at 90iterations 4.8523564E-03 0.1488962 at 100iterations 2.2902887E-03 6.6684246E-02 at 110iterations 1.0802230E-03 3.4912109E-02 at 120iterations finished qdiffx linear iterations at : 15:07:23 total time elapsed so far: 9.030000 # loops : 120 mean,max change (kT/e) : 1.0802230E-03 3.4912109E-02 energy calculations done at 9.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.160000 DelPhi exited at 15:07:23 9.159u 0.301s 0:09.82 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 Sat Oct 15 2011 at 15:07:23 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 = 2851 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.829539 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): -12.16400 36.64400 ymin,ymax (A): 3.357000 51.96000 zmin,zma (A): -11.14900 45.46800 x,y,z range (A): 48.80800 48.60300 56.61700 scale (grids/A): 2.829539 object centre (A): 12.24000 27.65850 17.15950 number of atom coordinates read : 2851 total number of charged atoms : 2704 net assigned charge : 3.500020 assigned positive charge : 431.9825 centred at (gu) : 91.39915 93.28876 98.02489 assigned negative charge : -428.4832 centred at (gu) : 90.43581 92.76568 97.78055 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 187377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23797 grid for indexing accessible points = 1.400000 m= 96232 mr = 138662 m= 33983 mr = 79434 m= 7572 mr = 27205 m= 958 mr = 5428 m= 72 mr = 589 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 587 time to turn everything in is 1.090000 number of dielectric boundary points 74853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 21630 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) : 1.886359 object centre at (A) : 12.24000 27.65850 17.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3081343 0.2449697 midg,1,midg; midg,igrid,midg -0.1709507 -3.0242739E-02 1,midg,midg; igrid,midg,midg -3.9717607E-02 0.4864713 gauss-seidel spectral radius is 0.9992564 estimated iterations to convergence 289 setup time was (sec) 1.400000 now iterating at: 15:07:25 rms-change max change #iterations 10.35447 402.2352 at 10iterations 6.061803 139.6530 at 20iterations 3.529053 72.77874 at 30iterations 2.047864 42.63094 at 40iterations 1.186753 22.82037 at 50iterations 0.6846948 13.51464 at 60iterations 0.3955291 7.205837 at 70iterations 0.2280676 4.369270 at 80iterations 0.1314494 2.359560 at 90iterations 7.5662047E-02 1.406414 at 100iterations 4.3589555E-02 0.7339439 at 110iterations 2.5117815E-02 0.4203110 at 120iterations 1.4429157E-02 0.2651329 at 130iterations 8.3020655E-03 0.1394138 at 140iterations 4.7759856E-03 9.0286255E-02 at 150iterations 2.7510496E-03 4.7042847E-02 at 160iterations 1.5900941E-03 2.7462006E-02 at 170iterations 9.1988832E-04 1.5434265E-02 at 180iterations finished qdiffx linear iterations at : 15:07:39 total time elapsed so far: 15.25000 # loops : 180 mean,max change (kT/e) : 9.1988832E-04 1.5434265E-02 energy calculations done at 15.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.39000 DelPhi exited at 15:07:39 15.387u 0.318s 0:16.06 97.6% 0+0k 0+0io 0pf+0w