Tue Oct 11 06:10:13 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+sph2.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 = amb2.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 06:10:13 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2070 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: 0.6862916 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): 19.52400 63.73700 ymin,ymax (A): 32.15400 84.02700 zmin,zma (A): 58.35600 97.96000 x,y,z range (A): 44.21300 51.87300 39.60400 scale (grids/A): 0.6862916 object centre (A): 41.63050 58.09050 78.15800 number of atom coordinates read : 2070 total number of charged atoms : 1942 net assigned charge : 7.500009 assigned positive charge : 316.2371 centred at (gu) : 89.73698 90.12540 88.91138 assigned negative charge : -308.7371 centred at (gu) : 89.87132 90.16206 88.84020 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6562 nv = 96 ne = 84 npr = 42117 no. pairs analyzed = 42117 no. exposed pairs = 2486 no. arc points = 16997 no. surface atoms = 863 nbur = 1207 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 384 mr = 3735 m= 5 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1678 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7505 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9949791E-08 4.7821491E-08 midg,1,midg; midg,igrid,midg 4.7767443E-08 2.7556025E-08 1,midg,midg; igrid,midg,midg 8.1999353E-08 -2.6967728E-09 gauss-seidel spectral radius is 0.9889362 estimated iterations to convergence 77 setup time was (sec) 0.4700000 now iterating at: 06:10:14 rms-change max change #iterations 0.1762745 23.54396 at 10iterations 2.0793406E-02 2.680218 at 20iterations 2.6642031E-03 0.4081621 at 30iterations 4.5776978E-04 6.7052841E-02 at 40iterations 1.1338653E-04 1.4278412E-02 at 50iterations finished qdiffx linear iterations at : 06:10:17 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.1338653E-04 1.4278412E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 06:10:17 3.242u 0.205s 0:03.90 88.2% 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 06:10:17 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2070 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: 2.058875 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): 19.52400 63.73700 ymin,ymax (A): 32.15400 84.02700 zmin,zma (A): 58.35600 97.96000 x,y,z range (A): 44.21300 51.87300 39.60400 scale (grids/A): 2.058875 object centre (A): 41.63050 58.09050 78.15800 number of atom coordinates read : 2070 total number of charged atoms : 1942 net assigned charge : 7.500009 assigned positive charge : 316.2371 centred at (gu) : 89.21088 90.37633 86.73440 assigned negative charge : -308.7371 centred at (gu) : 89.61405 90.48642 86.52065 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16997 grid for indexing accessible points = 1.400000 m= 27499 mr = 49506 m= 4814 mr = 20614 m= 369 mr = 2955 m= 10 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 559 time to turn everything in is 0.5200000 number of dielectric boundary points 29129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15382 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) : 0.6862916 object centre at (A) : 41.63050 58.09050 78.15800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6473260E-02 1.2424760E-02 midg,1,midg; midg,igrid,midg 2.3162793E-02 2.4255183E-02 1,midg,midg; igrid,midg,midg 5.8060262E-02 8.3252890E-03 gauss-seidel spectral radius is 0.9987642 estimated iterations to convergence 225 setup time was (sec) 0.8300000 now iterating at: 06:10:18 rms-change max change #iterations 4.370693 181.5798 at 10iterations 2.137169 68.73940 at 20iterations 1.039699 32.59391 at 30iterations 0.5074190 15.53310 at 40iterations 0.2480952 8.027491 at 50iterations 0.1211391 4.172014 at 60iterations 5.9132930E-02 1.799679 at 70iterations 2.8917482E-02 0.9056357 at 80iterations 1.4137541E-02 0.4781551 at 90iterations 6.9462657E-03 0.2163877 at 100iterations 3.4584543E-03 0.1255646 at 110iterations 1.7427114E-03 5.5174828E-02 at 120iterations finished qdiffx linear iterations at : 06:10:25 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.7427114E-03 5.5174828E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 06:10:26 7.457u 0.217s 0:08.34 91.8% 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 06:10:26 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2070 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: 3.088312 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): 19.52400 63.73700 ymin,ymax (A): 32.15400 84.02700 zmin,zma (A): 58.35600 97.96000 x,y,z range (A): 44.21300 51.87300 39.60400 scale (grids/A): 3.088312 object centre (A): 41.63050 58.09050 78.15800 number of atom coordinates read : 2070 total number of charged atoms : 1942 net assigned charge : 7.500009 assigned positive charge : 316.2371 centred at (gu) : 88.81633 90.56442 85.10150 assigned negative charge : -308.7371 centred at (gu) : 89.42104 90.72975 84.78103 start vw surface at 0.1400000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 160605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16997 grid for indexing accessible points = 1.400000 m= 86620 mr = 119201 m= 33897 mr = 71941 m= 8829 mr = 27365 m= 1440 mr = 6394 m= 171 mr = 954 m= 6 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 1780 time to turn everything in is 1.570000 number of dielectric boundary points 65625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 15536 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) : 2.058875 object centre at (A) : 41.63050 58.09050 78.15800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2582757 5.0416101E-02 midg,1,midg; midg,igrid,midg 0.1705573 0.1876175 1,midg,midg; igrid,midg,midg 0.6832412 5.1181920E-02 gauss-seidel spectral radius is 0.9992767 estimated iterations to convergence 293 setup time was (sec) 1.850000 now iterating at: 06:10:28 rms-change max change #iterations 9.880775 359.8817 at 10iterations 5.792053 160.0143 at 20iterations 3.393581 65.57924 at 30iterations 1.983583 51.68299 at 40iterations 1.160127 24.06833 at 50iterations 0.6739627 12.90984 at 60iterations 0.3926786 7.504704 at 70iterations 0.2289804 4.048792 at 80iterations 0.1330529 2.826820 at 90iterations 7.7291101E-02 1.592527 at 100iterations 4.4905130E-02 0.7949181 at 110iterations 2.6240975E-02 0.4680882 at 120iterations 1.5343618E-02 0.3179626 at 130iterations 9.0727871E-03 0.1715479 at 140iterations 5.4423301E-03 0.1078491 at 150iterations 3.3568195E-03 6.3819885E-02 at 160iterations 2.1698202E-03 4.0496826E-02 at 170iterations 1.4777194E-03 2.7858734E-02 at 180iterations finished qdiffx linear iterations at : 06:10:37 total time elapsed so far: 11.59000 # loops : 180 mean,max change (kT/e) : 1.4777194E-03 2.7858734E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.77000 DelPhi exited at 06:10:38 11.772u 0.220s 0:12.29 97.5% 0+0k 0+0io 0pf+0w