Tue Oct 11 05:50:21 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 05:50:21 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7311262 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): 25.61200 72.11700 ymin,ymax (A): -18.78000 29.91200 zmin,zma (A): 3.938000 46.39400 x,y,z range (A): 46.50500 48.69200 42.45600 scale (grids/A): 0.7311262 object centre (A): 48.86450 5.566001 25.16600 number of atom coordinates read : 2290 total number of charged atoms : 1967 net assigned charge : 6.039010 assigned positive charge : 320.3060 centred at (gu) : 89.17451 90.59255 90.28470 assigned negative charge : -314.2671 centred at (gu) : 89.31168 90.53040 90.36502 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7811 nv = 96 ne = 84 npr = 41679 no. pairs analyzed = 41679 no. exposed pairs = 2579 no. arc points = 17597 no. surface atoms = 883 nbur = 1407 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 547 mr = 4576 m= 8 mr = 108 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 0.2700000 number of dielectric boundary points 3682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1536 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4477214E-07 2.0084464E-08 midg,1,midg; midg,igrid,midg 3.1407254E-08 1.5396324E-07 1,midg,midg; igrid,midg,midg 2.3260746E-07 -2.3892664E-08 gauss-seidel spectral radius is 0.9902452 estimated iterations to convergence 82 setup time was (sec) 0.5100000 now iterating at: 05:50:22 rms-change max change #iterations 0.2311146 33.48572 at 10iterations 3.1175883E-02 4.026318 at 20iterations 4.6710349E-03 0.6076889 at 30iterations 9.6524507E-04 0.1125946 at 40iterations 2.8804742E-04 2.9699326E-02 at 50iterations finished qdiffx linear iterations at : 05:50:24 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 2.8804742E-04 2.9699326E-02 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 05:50:25 3.240u 0.190s 0:03.80 90.2% 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 05:50:25 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.193379 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): 25.61200 72.11700 ymin,ymax (A): -18.78000 29.91200 zmin,zma (A): 3.938000 46.39400 x,y,z range (A): 46.50500 48.69200 42.45600 scale (grids/A): 2.193379 object centre (A): 48.86450 5.566001 25.16600 number of atom coordinates read : 2290 total number of charged atoms : 1967 net assigned charge : 6.039010 assigned positive charge : 320.3060 centred at (gu) : 87.52385 91.77778 90.85401 assigned negative charge : -314.2671 centred at (gu) : 87.93511 91.59125 91.09530 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 81801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17597 grid for indexing accessible points = 1.400000 m= 34833 mr = 58754 m= 7334 mr = 26778 m= 777 mr = 5022 m= 30 mr = 417 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 33800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15635 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) : 0.7311262 object centre at (A) : 48.86450 5.566001 25.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4645481E-02 3.0150006E-02 midg,1,midg; midg,igrid,midg 4.3084443E-02 3.2329019E-02 1,midg,midg; igrid,midg,midg 5.0675534E-02 -5.6287203E-02 gauss-seidel spectral radius is 0.9988986 estimated iterations to convergence 238 setup time was (sec) 0.9600000 now iterating at: 05:50:26 rms-change max change #iterations 4.931649 198.0233 at 10iterations 2.492211 99.03345 at 20iterations 1.262383 36.27404 at 30iterations 0.6392909 19.84530 at 40iterations 0.3240240 8.994170 at 50iterations 0.1647296 4.660474 at 60iterations 8.3767965E-02 2.391347 at 70iterations 4.2792510E-02 1.192858 at 80iterations 2.1885907E-02 0.5752144 at 90iterations 1.1402794E-02 0.3851585 at 100iterations 6.0054972E-03 0.1777997 at 110iterations 3.3077265E-03 9.9975586E-02 at 120iterations finished qdiffx linear iterations at : 05:50:34 total time elapsed so far: 8.550000 # loops : 120 mean,max change (kT/e) : 3.3077265E-03 9.9975586E-02 energy calculations done at 8.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 05:50:35 8.743u 0.262s 0:09.71 92.6% 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 Tue Oct 11 2011 at 05:50:35 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.290068 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): 25.61200 72.11700 ymin,ymax (A): -18.78000 29.91200 zmin,zma (A): 3.938000 46.39400 x,y,z range (A): 46.50500 48.69200 42.45600 scale (grids/A): 3.290068 object centre (A): 48.86450 5.566001 25.16600 number of atom coordinates read : 2290 total number of charged atoms : 1967 net assigned charge : 6.039010 assigned positive charge : 320.3060 centred at (gu) : 86.28565 92.66669 91.28115 assigned negative charge : -314.2671 centred at (gu) : 86.90269 92.38699 91.64287 start vw surface at 0.1300000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 188054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17597 grid for indexing accessible points = 1.400000 m= 106204 mr = 140726 m= 46215 mr = 89311 m= 14185 mr = 38474 m= 3085 mr = 11063 m= 371 mr = 2246 m= 16 mr = 226 m= 0 mr = 9 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 76075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 15732 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) : 2.193379 object centre at (A) : 48.86450 5.566001 25.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1094291 0.2568518 midg,1,midg; midg,igrid,midg 0.3069231 0.1739991 1,midg,midg; igrid,midg,midg 0.4761041 -0.6652258 gauss-seidel spectral radius is 0.9993153 estimated iterations to convergence 301 setup time was (sec) 2.180000 now iterating at: 05:50:37 rms-change max change #iterations 10.83237 388.8747 at 10iterations 6.470280 135.2892 at 20iterations 3.851624 77.52559 at 30iterations 2.294151 41.22333 at 40iterations 1.361816 26.79779 at 50iterations 0.8062471 14.36150 at 60iterations 0.4778330 9.611713 at 70iterations 0.2827333 5.012790 at 80iterations 0.1672523 2.690744 at 90iterations 9.8879337E-02 1.669115 at 100iterations 5.8681041E-02 1.038204 at 110iterations 3.5040978E-02 0.5934467 at 120iterations 2.1107273E-02 0.3385696 at 130iterations 1.2975158E-02 0.2752609 at 140iterations 8.2630757E-03 0.1534195 at 150iterations 5.5168564E-03 9.7602844E-02 at 160iterations 3.9308663E-03 7.5515747E-02 at 170iterations 2.9736974E-03 5.3840637E-02 at 180iterations finished qdiffx linear iterations at : 05:50:47 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 2.9736974E-03 5.3840637E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 05:50:48 12.364u 0.175s 0:12.87 97.3% 0+0k 0+0io 0pf+0w