Mon Oct 10 00:41:07 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 Mon Oct 10 2011 at 00:41:07 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 = 2210 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: 0.6870332 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): -9.566000 42.25100 ymin,ymax (A): -52.47000 -3.719000 zmin,zma (A): -23.75600 24.34100 x,y,z range (A): 51.81700 48.75100 48.09700 scale (grids/A): 0.6870332 object centre (A): 16.34250 -28.09450 0.2924995 number of atom coordinates read : 2210 total number of charged atoms : 2068 net assigned charge : 5.000012 assigned positive charge : 328.6696 centred at (gu) : 88.62232 89.02577 90.30566 assigned negative charge : -323.6699 centred at (gu) : 88.48642 89.02572 90.30128 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7260 nv = 96 ne = 84 npr = 43914 no. pairs analyzed = 43914 no. exposed pairs = 3070 no. arc points = 21264 no. surface atoms = 1036 nbur = 1174 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 3741 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1892 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8025 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3485802E-08 2.9407307E-08 midg,1,midg; midg,igrid,midg 3.1780683E-08 2.1829020E-08 1,midg,midg; igrid,midg,midg -2.4226710E-08 5.2620216E-08 gauss-seidel spectral radius is 0.9889880 estimated iterations to convergence 78 setup time was (sec) 0.3900000 now iterating at: 00:41:08 rms-change max change #iterations 0.1856409 28.09070 at 10iterations 2.1263333E-02 2.911564 at 20iterations 2.4210694E-03 0.3657322 at 30iterations 2.8301310E-04 3.6749840E-02 at 40iterations 3.5030716E-05 5.0001144E-03 at 50iterations finished qdiffx linear iterations at : 00:41:11 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.5030716E-05 5.0001144E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 00:41:11 3.435u 0.172s 0:03.93 91.6% 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 Mon Oct 10 2011 at 00:41:11 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 = 2210 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: 2.061100 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): -9.566000 42.25100 ymin,ymax (A): -52.47000 -3.719000 zmin,zma (A): -23.75600 24.34100 x,y,z range (A): 51.81700 48.75100 48.09700 scale (grids/A): 2.061100 object centre (A): 16.34250 -28.09450 0.2924995 number of atom coordinates read : 2210 total number of charged atoms : 2068 net assigned charge : 5.000012 assigned positive charge : 328.6696 centred at (gu) : 85.86670 87.07705 90.91660 assigned negative charge : -323.6699 centred at (gu) : 85.45932 87.07700 90.90369 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21264 grid for indexing accessible points = 1.400000 m= 28232 mr = 51357 m= 5531 mr = 20136 m= 505 mr = 3558 m= 18 mr = 257 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 35674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 16400 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) : 0.6870332 object centre at (A) : 16.34250 -28.09450 0.2924995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4035772E-02 2.8348364E-02 midg,1,midg; midg,igrid,midg 1.1119014E-02 -2.2216324E-02 1,midg,midg; igrid,midg,midg 1.4444952E-02 3.2486424E-02 gauss-seidel spectral radius is 0.9988050 estimated iterations to convergence 229 setup time was (sec) 0.6100000 now iterating at: 00:41:12 rms-change max change #iterations 4.512047 184.4529 at 10iterations 2.201606 76.81392 at 20iterations 1.084991 36.22453 at 30iterations 0.5332725 15.21403 at 40iterations 0.2616300 7.739339 at 50iterations 0.1284510 3.996889 at 60iterations 6.3103102E-02 1.890236 at 70iterations 3.1027483E-02 0.8991795 at 80iterations 1.5267373E-02 0.4867630 at 90iterations 7.4986462E-03 0.2432833 at 100iterations 3.6890293E-03 0.1127534 at 110iterations 1.8139753E-03 6.1332703E-02 at 120iterations finished qdiffx linear iterations at : 00:41:19 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.8139753E-03 6.1332703E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 00:41:20 7.976u 0.197s 0:08.44 96.6% 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 Mon Oct 10 2011 at 00:41:20 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 = 2210 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: 3.091649 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): -9.566000 42.25100 ymin,ymax (A): -52.47000 -3.719000 zmin,zma (A): -23.75600 24.34100 x,y,z range (A): 51.81700 48.75100 48.09700 scale (grids/A): 3.091649 object centre (A): 16.34250 -28.09450 0.2924995 number of atom coordinates read : 2210 total number of charged atoms : 2068 net assigned charge : 5.000012 assigned positive charge : 328.6696 centred at (gu) : 83.80003 85.61562 91.37501 assigned negative charge : -323.6699 centred at (gu) : 83.18891 85.61541 91.35555 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 177229 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21264 grid for indexing accessible points = 1.400000 m= 88260 mr = 125218 m= 35071 mr = 70311 m= 10207 mr = 27767 m= 2058 mr = 7731 m= 253 mr = 1478 m= 14 mr = 180 m= 0 mr = 4 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 80403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 16544 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) : 2.061100 object centre at (A) : 16.34250 -28.09450 0.2924995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7493511 0.2209191 midg,1,midg; midg,igrid,midg 5.5811364E-02 -0.3772305 1,midg,midg; igrid,midg,midg 0.2318385 0.2657023 gauss-seidel spectral radius is 0.9993074 estimated iterations to convergence 300 setup time was (sec) 1.410000 now iterating at: 00:41:21 rms-change max change #iterations 10.26737 469.6134 at 10iterations 6.118065 126.9723 at 20iterations 3.633547 78.83913 at 30iterations 2.154174 40.59805 at 40iterations 1.271932 22.60638 at 50iterations 0.7509401 13.30381 at 60iterations 0.4414854 8.295048 at 70iterations 0.2590357 4.955142 at 80iterations 0.1524947 2.837214 at 90iterations 8.9389302E-02 1.625412 at 100iterations 5.2508574E-02 0.9356104 at 110iterations 3.0745188E-02 0.5463977 at 120iterations 1.8028047E-02 0.3151131 at 130iterations 1.0545675E-02 0.1891727 at 140iterations 6.1822804E-03 0.1273041 at 150iterations 3.6155044E-03 6.3228607E-02 at 160iterations 2.1213084E-03 3.5495758E-02 at 170iterations 1.2415432E-03 2.2186279E-02 at 180iterations finished qdiffx linear iterations at : 00:41:33 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 1.2415432E-03 2.2186279E-02 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 00:41:33 13.079u 0.206s 0:13.59 97.6% 0+0k 0+0io 0pf+0w