Tue Oct 11 06:26:56 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 06:26:56 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 = 2034 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7508806 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): 25.66400 72.07400 ymin,ymax (A): -18.71800 28.69300 zmin,zma (A): 4.018000 46.44400 x,y,z range (A): 46.41000 47.41100 42.42600 scale (grids/A): 0.7508806 object centre (A): 48.86900 4.987499 25.23100 number of atom coordinates read : 2034 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.19353 90.74816 90.16670 assigned negative charge : -304.2972 centred at (gu) : 89.34255 90.63284 90.23196 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7989 nv = 96 ne = 84 npr = 40448 no. pairs analyzed = 40448 no. exposed pairs = 2483 no. arc points = 17006 no. surface atoms = 848 nbur = 1186 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 612 mr = 4713 m= 7 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1485 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 8358 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3499292E-07 8.7757918E-08 midg,1,midg; midg,igrid,midg 2.2290166E-08 3.4574205E-07 1,midg,midg; igrid,midg,midg 3.9554098E-07 -1.3511907E-08 gauss-seidel spectral radius is 0.9907417 estimated iterations to convergence 84 setup time was (sec) 0.4600000 now iterating at: 06:26:56 rms-change max change #iterations 0.2563537 31.29895 at 10iterations 3.5685889E-02 4.491288 at 20iterations 5.1792599E-03 0.7286339 at 30iterations 8.2301075E-04 0.1063976 at 40iterations 1.8621875E-04 2.3168564E-02 at 50iterations finished qdiffx linear iterations at : 06:26:59 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 1.8621875E-04 2.3168564E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 06:27:00 3.193u 0.152s 0:03.86 86.5% 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 06:27:00 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 = 2034 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: 2.252642 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): 25.66400 72.07400 ymin,ymax (A): -18.71800 28.69300 zmin,zma (A): 4.018000 46.44400 x,y,z range (A): 46.41000 47.41100 42.42600 scale (grids/A): 2.252642 object centre (A): 48.86900 4.987499 25.23100 number of atom coordinates read : 2034 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 87.58053 92.24428 90.50026 assigned negative charge : -304.2972 centred at (gu) : 88.02798 91.89883 90.69600 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 83278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17006 grid for indexing accessible points = 1.400000 m= 36260 mr = 59655 m= 8164 mr = 28343 m= 940 mr = 5762 m= 38 mr = 562 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 34354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15371 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) : 0.7508806 object centre at (A) : 48.86900 4.987499 25.23100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8073125E-02 3.5884105E-02 midg,1,midg; midg,igrid,midg 5.2486513E-02 0.1154728 1,midg,midg; igrid,midg,midg 6.1134171E-02 -6.3228071E-02 gauss-seidel spectral radius is 0.9989393 estimated iterations to convergence 243 setup time was (sec) 0.8900000 now iterating at: 06:27:01 rms-change max change #iterations 5.007638 185.8850 at 10iterations 2.565662 87.23041 at 20iterations 1.314578 39.37830 at 30iterations 0.6758986 21.25876 at 40iterations 0.3472732 9.212690 at 50iterations 0.1777737 4.893829 at 60iterations 9.1548093E-02 2.843933 at 70iterations 4.6899311E-02 1.247093 at 80iterations 2.4252448E-02 0.7037106 at 90iterations 1.2540678E-02 0.3307829 at 100iterations 6.4921230E-03 0.2030034 at 110iterations 3.4103442E-03 9.3631744E-02 at 120iterations finished qdiffx linear iterations at : 06:27:07 total time elapsed so far: 6.960000 # loops : 120 mean,max change (kT/e) : 3.4103442E-03 9.3631744E-02 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 06:27:07 7.127u 0.191s 0:07.84 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 Tue Oct 11 2011 at 06:27:07 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 = 2034 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.378963 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): 25.66400 72.07400 ymin,ymax (A): -18.71800 28.69300 zmin,zma (A): 4.018000 46.44400 x,y,z range (A): 46.41000 47.41100 42.42600 scale (grids/A): 3.378963 object centre (A): 48.86900 4.987499 25.23100 number of atom coordinates read : 2034 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 86.37084 93.36634 90.75040 assigned negative charge : -304.2972 centred at (gu) : 87.04187 92.84829 91.04409 start vw surface at 0.1100000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 191202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17006 grid for indexing accessible points = 1.400000 m= 109319 mr = 142898 m= 49137 mr = 92246 m= 15953 mr = 41296 m= 3832 mr = 12872 m= 625 mr = 2945 m= 45 mr = 475 m= 0 mr = 18 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.960000 number of dielectric boundary points 77363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 15432 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) : 2.252642 object centre at (A) : 48.86900 4.987499 25.23100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1216433 0.2793319 midg,1,midg; midg,igrid,midg 0.3875516 0.7848372 1,midg,midg; igrid,midg,midg 0.5339515 -0.7149574 gauss-seidel spectral radius is 0.9993244 estimated iterations to convergence 303 setup time was (sec) 2.280000 now iterating at: 06:27:10 rms-change max change #iterations 10.88968 250.6364 at 10iterations 6.514432 117.3816 at 20iterations 3.893237 69.58765 at 30iterations 2.318979 43.30407 at 40iterations 1.382416 24.38461 at 50iterations 0.8211086 15.35057 at 60iterations 0.4859942 8.276031 at 70iterations 0.2887100 5.740260 at 80iterations 0.1715202 2.893101 at 90iterations 0.1016418 1.861328 at 100iterations 6.0290650E-02 0.9986753 at 110iterations 3.5925701E-02 0.5770950 at 120iterations 2.1524448E-02 0.3812084 at 130iterations 1.3048464E-02 0.2073002 at 140iterations 8.0821877E-03 0.1466827 at 150iterations 5.2197794E-03 9.3936920E-02 at 160iterations 3.5095140E-03 6.3606262E-02 at 170iterations 2.5159889E-03 4.5154572E-02 at 180iterations finished qdiffx linear iterations at : 06:27:21 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 2.5159889E-03 4.5154572E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 06:27:22 13.569u 0.233s 0:14.32 96.2% 0+0k 0+0io 0pf+0w