Wed Feb 15 08:56:08 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:08 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 = 2474 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: 0.6295760 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): -19.90800 34.09200 ymin,ymax (A): -25.85500 30.69100 zmin,zma (A): -10.61900 39.34100 x,y,z range (A): 54.00000 56.54600 49.96000 scale (grids/A): 0.6295760 object centre (A): 7.092002 2.418000 14.36100 number of atom coordinates read : 2474 total number of charged atoms : 2336 net assigned charge : 8.500010 assigned positive charge : 367.4230 centred at (gu) : 90.76351 90.24457 90.50198 assigned negative charge : -358.9238 centred at (gu) : 90.91140 90.38605 90.31001 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6477 nv = 96 ne = 84 npr = 50586 no. pairs analyzed = 50586 no. exposed pairs = 3130 no. arc points = 22038 no. surface atoms = 1067 nbur = 1407 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3359 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2800000 number of dielectric boundary points 3432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2266 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8907852E-09 2.7204823E-08 midg,1,midg; midg,igrid,midg 1.9406496E-08 -2.5684317E-09 1,midg,midg; igrid,midg,midg 1.7782583E-08 -3.5846752E-09 gauss-seidel spectral radius is 0.9869212 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 08:56:09 rms-change max change #iterations 0.1256460 22.01742 at 10iterations 1.1759564E-02 1.677359 at 20iterations 1.1263086E-03 0.1732330 at 30iterations 1.1973243E-04 1.9083977E-02 at 40iterations 1.7025919E-05 2.9954910E-03 at 50iterations finished qdiffx linear iterations at : 08:56:11 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.7025919E-05 2.9954910E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:56:12 3.376u 0.164s 0:04.42 79.8% 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 Wed Feb 15 2012 at 08:56:12 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 = 2474 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: 1.888728 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): -19.90800 34.09200 ymin,ymax (A): -25.85500 30.69100 zmin,zma (A): -10.61900 39.34100 x,y,z range (A): 54.00000 56.54600 49.96000 scale (grids/A): 1.888728 object centre (A): 7.092002 2.418000 14.36100 number of atom coordinates read : 2474 total number of charged atoms : 2336 net assigned charge : 8.500010 assigned positive charge : 367.4230 centred at (gu) : 92.28998 90.73296 91.50560 assigned negative charge : -358.9238 centred at (gu) : 92.73422 91.15813 90.92984 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 70186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22038 grid for indexing accessible points = 1.400000 m= 23621 mr = 47467 m= 3360 mr = 16398 m= 206 mr = 1870 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 676 time to turn everything in is 0.5500000 number of dielectric boundary points 31571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18333 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) : 0.6295760 object centre at (A) : 7.092002 2.418000 14.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9547509E-03 4.1154485E-02 midg,1,midg; midg,igrid,midg 2.3346858E-02 -3.8154379E-02 1,midg,midg; igrid,midg,midg 3.0386379E-02 5.0509614E-03 gauss-seidel spectral radius is 0.9985948 estimated iterations to convergence 211 setup time was (sec) 0.8400000 now iterating at: 08:56:13 rms-change max change #iterations 3.955481 165.1099 at 10iterations 1.826058 63.70185 at 20iterations 0.8487067 31.22299 at 30iterations 0.3925497 12.69939 at 40iterations 0.1821076 6.151722 at 50iterations 8.4062792E-02 2.732536 at 60iterations 3.8925271E-02 1.288784 at 70iterations 1.8069280E-02 0.6216021 at 80iterations 8.3287749E-03 0.2638774 at 90iterations 3.8686206E-03 0.1301117 at 100iterations 1.7995776E-03 5.8189392E-02 at 110iterations 8.3509320E-04 2.8202057E-02 at 120iterations finished qdiffx linear iterations at : 08:56:21 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 8.3509320E-04 2.8202057E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 08:56:21 8.303u 0.225s 0:09.01 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 Wed Feb 15 2012 at 08:56:21 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 = 2474 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.833092 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): -19.90800 34.09200 ymin,ymax (A): -25.85500 30.69100 zmin,zma (A): -10.61900 39.34100 x,y,z range (A): 54.00000 56.54600 49.96000 scale (grids/A): 2.833092 object centre (A): 7.092002 2.418000 14.36100 number of atom coordinates read : 2474 total number of charged atoms : 2336 net assigned charge : 8.500010 assigned positive charge : 367.4230 centred at (gu) : 93.43488 91.09930 92.25829 assigned negative charge : -358.9238 centred at (gu) : 94.10116 91.73704 91.39471 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 162393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22038 grid for indexing accessible points = 1.400000 m= 78189 mr = 115779 m= 25883 mr = 62184 m= 5998 mr = 19605 m= 862 mr = 4158 m= 44 mr = 533 m= 0 mr = 13 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 2155 time to turn everything in is 1.410000 number of dielectric boundary points 71097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 18688 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) : 1.888728 object centre at (A) : 7.092002 2.418000 14.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4858700E-02 0.4632106 midg,1,midg; midg,igrid,midg 0.3243382 -0.5260837 1,midg,midg; igrid,midg,midg 0.4005312 5.4142334E-02 gauss-seidel spectral radius is 0.9992517 estimated iterations to convergence 289 setup time was (sec) 1.750000 now iterating at: 08:56:23 rms-change max change #iterations 9.490360 341.2272 at 10iterations 5.571471 127.9490 at 20iterations 3.226464 69.51031 at 30iterations 1.872674 41.91979 at 40iterations 1.081174 21.45420 at 50iterations 0.6232794 12.62355 at 60iterations 0.3591232 6.798739 at 70iterations 0.2060158 4.061586 at 80iterations 0.1182538 2.388063 at 90iterations 6.7987062E-02 1.364037 at 100iterations 3.8998086E-02 0.7341809 at 110iterations 2.2394031E-02 0.4277415 at 120iterations 1.2834943E-02 0.2373333 at 130iterations 7.3419944E-03 0.1358643 at 140iterations 4.2096414E-03 9.1971397E-02 at 150iterations 2.4129441E-03 4.7478676E-02 at 160iterations 1.3805582E-03 2.4969101E-02 at 170iterations 7.9077407E-04 1.5490532E-02 at 180iterations finished qdiffx linear iterations at : 08:56:35 total time elapsed so far: 13.62000 # loops : 180 mean,max change (kT/e) : 7.9077407E-04 1.5490532E-02 energy calculations done at 13.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.82000 DelPhi exited at 08:56:36 13.823u 0.219s 0:14.51 96.6% 0+0k 0+0io 0pf+0w