Mon Oct 10 14:10:40 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 Mon Oct 10 2011 at 14:10:40 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2181 !!! WARNING: ASL 36 has a net charge of -0.1000 !!! WARNING: LYS 209 has a net charge of -0.2720 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: 0.6487826 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): -22.03300 24.21200 ymin,ymax (A): -53.41900 -8.839001 zmin,zma (A): -34.72500 20.14700 x,y,z range (A): 46.24500 44.58000 54.87200 scale (grids/A): 0.6487826 object centre (A): 1.089500 -31.12900 -7.288999 number of atom coordinates read : 2181 total number of charged atoms : 2040 net assigned charge : -7.371979 assigned positive charge : 330.7437 centred at (gu) : 89.34785 90.60341 91.60668 assigned negative charge : -338.1158 centred at (gu) : 89.37888 90.65530 91.72582 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6170 nv = 96 ne = 84 npr = 44278 no. pairs analyzed = 44278 no. exposed pairs = 2868 no. arc points = 20458 no. surface atoms = 965 nbur = 1216 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3224 m= 0 mr = 24 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1911 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7266 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9871733E-10 -4.0622876E-08 midg,1,midg; midg,igrid,midg -6.0588308E-09 -2.2798368E-08 1,midg,midg; igrid,midg,midg -1.0763135E-08 -1.5221577E-08 gauss-seidel spectral radius is 0.9876558 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 14:10:41 rms-change max change #iterations 0.1470879 24.28686 at 10iterations 1.5087051E-02 2.254477 at 20iterations 1.5121184E-03 0.2676105 at 30iterations 1.5555041E-04 2.3864746E-02 at 40iterations 1.5672453E-05 2.3269653E-03 at 50iterations finished qdiffx linear iterations at : 14:10:46 total time elapsed so far: 5.430000 # loops : 50 mean,max change (kT/e) : 1.5672453E-05 2.3269653E-03 energy calculations done at 5.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.610000 DelPhi exited at 14:10:47 5.615u 0.435s 0:06.37 94.8% 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 Mon Oct 10 2011 at 14:10:47 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2181 !!! WARNING: ASL 36 has a net charge of -0.1000 !!! WARNING: LYS 209 has a net charge of -0.2720 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: 1.946348 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): -22.03300 24.21200 ymin,ymax (A): -53.41900 -8.839001 zmin,zma (A): -34.72500 20.14700 x,y,z range (A): 46.24500 44.58000 54.87200 scale (grids/A): 1.946348 object centre (A): 1.089500 -31.12900 -7.288999 number of atom coordinates read : 2181 total number of charged atoms : 2040 net assigned charge : -7.371979 assigned positive charge : 330.7437 centred at (gu) : 88.04350 91.81006 94.81988 assigned negative charge : -338.1158 centred at (gu) : 88.13651 91.96588 95.17746 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66350 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20458 grid for indexing accessible points = 1.400000 m= 23037 mr = 44424 m= 3560 mr = 16469 m= 193 mr = 2168 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 30030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 16083 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) : 0.6487826 object centre at (A) : 1.089500 -31.12900 -7.288999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3287701E-02 -9.6209042E-02 midg,1,midg; midg,igrid,midg -1.4030260E-02 -2.0268334E-02 1,midg,midg; igrid,midg,midg 3.1251735E-03 -1.4602114E-03 gauss-seidel spectral radius is 0.9986539 estimated iterations to convergence 216 setup time was (sec) 0.9500000 now iterating at: 14:10:48 rms-change max change #iterations 4.093926 188.7525 at 10iterations 1.919616 67.97253 at 20iterations 0.9025924 31.27829 at 30iterations 0.4241220 14.86873 at 40iterations 0.1985429 6.226749 at 50iterations 9.3445472E-02 2.956238 at 60iterations 4.3960087E-02 1.490112 at 70iterations 2.0633005E-02 0.6719570 at 80iterations 9.7171608E-03 0.2989922 at 90iterations 4.5715775E-03 0.1570158 at 100iterations 2.1536266E-03 6.9312096E-02 at 110iterations 1.0109975E-03 3.2119751E-02 at 120iterations finished qdiffx linear iterations at : 14:11:01 total time elapsed so far: 13.87000 # loops : 120 mean,max change (kT/e) : 1.0109975E-03 3.2119751E-02 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.04000 DelPhi exited at 14:11:02 14.044u 0.509s 0:14.83 98.0% 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 14:11:02 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2181 !!! WARNING: ASL 36 has a net charge of -0.1000 !!! WARNING: LYS 209 has a net charge of -0.2720 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: 2.919522 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): -22.03300 24.21200 ymin,ymax (A): -53.41900 -8.839001 zmin,zma (A): -34.72500 20.14700 x,y,z range (A): 46.24500 44.58000 54.87200 scale (grids/A): 2.919522 object centre (A): 1.089500 -31.12900 -7.288999 number of atom coordinates read : 2181 total number of charged atoms : 2040 net assigned charge : -7.371979 assigned positive charge : 330.7437 centred at (gu) : 87.06522 92.71503 97.22985 assigned negative charge : -338.1158 centred at (gu) : 87.20469 92.94885 97.76617 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 153170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20458 grid for indexing accessible points = 1.400000 m= 74747 mr = 108006 m= 26456 mr = 59781 m= 6352 mr = 20866 m= 800 mr = 4698 m= 26 mr = 505 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 67689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 16319 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) : 1.946348 object centre at (A) : 1.089500 -31.12900 -7.288999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1827388 -1.119192 midg,1,midg; midg,igrid,midg -0.1424778 -0.1832728 1,midg,midg; igrid,midg,midg 4.2300422E-02 -1.0603246E-02 gauss-seidel spectral radius is 0.9992552 estimated iterations to convergence 289 setup time was (sec) 1.880000 now iterating at: 14:11:04 rms-change max change #iterations 9.491199 387.3098 at 10iterations 5.481873 115.8262 at 20iterations 3.145663 66.37222 at 30iterations 1.807678 36.61021 at 40iterations 1.038008 20.71471 at 50iterations 0.5948613 11.94073 at 60iterations 0.3408082 7.530154 at 70iterations 0.1954044 3.719537 at 80iterations 0.1116029 2.357159 at 90iterations 6.3990496E-02 1.418409 at 100iterations 3.6587153E-02 0.6972542 at 110iterations 2.0957598E-02 0.4109497 at 120iterations 1.2004953E-02 0.2350998 at 130iterations 6.8545360E-03 0.1266098 at 140iterations 3.9249323E-03 8.0005646E-02 at 150iterations 2.2533259E-03 4.1570663E-02 at 160iterations 1.2865858E-03 2.6016235E-02 at 170iterations 7.3812547E-04 1.5548706E-02 at 180iterations finished qdiffx linear iterations at : 14:11:24 total time elapsed so far: 21.97000 # loops : 180 mean,max change (kT/e) : 7.3812547E-04 1.5548706E-02 energy calculations done at 21.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.13000 DelPhi exited at 14:11:25 22.136u 0.550s 0:23.04 98.4% 0+0k 0+0io 0pf+0w