Sat Oct 15 14:58:41 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 Sat Oct 15 2011 at 14:58:41 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2434 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: 0.6421819 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): -35.06500 10.52000 ymin,ymax (A): -16.79500 38.64100 zmin,zma (A): -44.49000 10.83400 x,y,z range (A): 45.58500 55.43600 55.32400 scale (grids/A): 0.6421819 object centre (A): -12.27250 10.92300 -16.82800 number of atom coordinates read : 2434 total number of charged atoms : 2299 net assigned charge : -2.999991 assigned positive charge : 362.9060 centred at (gu) : 89.23241 89.16706 90.15990 assigned negative charge : -365.9069 centred at (gu) : 89.20560 89.29070 90.15199 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7043 nv = 96 ne = 84 npr = 48257 no. pairs analyzed = 48257 no. exposed pairs = 3378 no. arc points = 24140 no. surface atoms = 1105 nbur = 1329 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 3560 m= 5 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2317 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8155 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4838130E-09 -3.9484309E-09 midg,1,midg; midg,igrid,midg 1.1428693E-08 -1.6199513E-08 1,midg,midg; igrid,midg,midg -9.2708801E-09 -1.4137532E-09 gauss-seidel spectral radius is 0.9874358 estimated iterations to convergence 73 setup time was (sec) 0.4700000 now iterating at: 14:58:42 rms-change max change #iterations 0.1458108 24.42553 at 10iterations 1.4473634E-02 2.201321 at 20iterations 1.4158165E-03 0.1898117 at 30iterations 1.4444918E-04 2.0699024E-02 at 40iterations 1.4586126E-05 2.6931763E-03 at 50iterations finished qdiffx linear iterations at : 14:58:45 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.4586126E-05 2.6931763E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 14:58:46 4.027u 0.277s 0:04.65 92.2% 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 Sat Oct 15 2011 at 14:58:46 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2434 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: 1.926546 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): -35.06500 10.52000 ymin,ymax (A): -16.79500 38.64100 zmin,zma (A): -44.49000 10.83400 x,y,z range (A): 45.58500 55.43600 55.32400 scale (grids/A): 1.926546 object centre (A): -12.27250 10.92300 -16.82800 number of atom coordinates read : 2434 total number of charged atoms : 2299 net assigned charge : -2.999991 assigned positive charge : 362.9060 centred at (gu) : 87.69677 87.50063 90.47906 assigned negative charge : -365.9069 centred at (gu) : 87.61660 87.87210 90.45596 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24140 grid for indexing accessible points = 1.400000 m= 26524 mr = 48847 m= 4479 mr = 18515 m= 254 mr = 2562 m= 7 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 35500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 18135 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) : 0.6421819 object centre at (A) : -12.27250 10.92300 -16.82800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6870922E-02 -5.6714383E-03 midg,1,midg; midg,igrid,midg 2.2780407E-02 -1.0098916E-02 1,midg,midg; igrid,midg,midg -1.3329585E-02 9.6822269E-03 gauss-seidel spectral radius is 0.9986680 estimated iterations to convergence 217 setup time was (sec) 0.7200000 now iterating at: 14:58:47 rms-change max change #iterations 4.209935 184.5267 at 10iterations 1.982310 79.43739 at 20iterations 0.9313619 31.15531 at 30iterations 0.4394825 14.02418 at 40iterations 0.2071810 6.957382 at 50iterations 9.7617216E-02 3.185143 at 60iterations 4.6038728E-02 1.416274 at 70iterations 2.1788711E-02 0.7986479 at 80iterations 1.0278812E-02 0.4001694 at 90iterations 4.8595355E-03 0.1734338 at 100iterations 2.2916172E-03 6.9069862E-02 at 110iterations 1.0822333E-03 3.6311150E-02 at 120iterations finished qdiffx linear iterations at : 14:58:56 total time elapsed so far: 9.690000 # loops : 120 mean,max change (kT/e) : 1.0822333E-03 3.6311150E-02 energy calculations done at 9.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 14:58:57 9.832u 0.352s 0:10.98 92.7% 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 Sat Oct 15 2011 at 14:58:57 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2434 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: 2.889819 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): -35.06500 10.52000 ymin,ymax (A): -16.79500 38.64100 zmin,zma (A): -44.49000 10.83400 x,y,z range (A): 45.58500 55.43600 55.32400 scale (grids/A): 2.889819 object centre (A): -12.27250 10.92300 -16.82800 number of atom coordinates read : 2434 total number of charged atoms : 2299 net assigned charge : -2.999991 assigned positive charge : 362.9060 centred at (gu) : 86.54501 86.25088 90.71837 assigned negative charge : -365.9069 centred at (gu) : 86.42494 86.80809 90.68394 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 171407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24140 grid for indexing accessible points = 1.400000 m= 83876 mr = 118971 m= 31626 mr = 66379 m= 7871 mr = 24346 m= 1095 mr = 5531 m= 76 mr = 650 m= 2 mr = 27 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 80050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 18386 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) : 1.926546 object centre at (A) : -12.27250 10.92300 -16.82800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8784262 -6.7549884E-02 midg,1,midg; midg,igrid,midg 0.2644886 -0.1018303 1,midg,midg; igrid,midg,midg -0.1547226 9.0788715E-02 gauss-seidel spectral radius is 0.9992713 estimated iterations to convergence 292 setup time was (sec) 1.240000 now iterating at: 14:58:58 rms-change max change #iterations 9.911964 360.2194 at 10iterations 5.783977 129.3230 at 20iterations 3.368288 68.62886 at 30iterations 1.952574 38.95564 at 40iterations 1.130642 21.63655 at 50iterations 0.6542007 12.31131 at 60iterations 0.3791553 7.363647 at 70iterations 0.2186535 4.107286 at 80iterations 0.1266504 2.393224 at 90iterations 7.3200330E-02 1.456226 at 100iterations 4.2109132E-02 0.7860489 at 110iterations 2.4298199E-02 0.4604607 at 120iterations 1.3975300E-02 0.2500648 at 130iterations 8.0752252E-03 0.1441731 at 140iterations 4.6648607E-03 8.7196350E-02 at 150iterations 2.6804104E-03 5.3939819E-02 at 160iterations 1.5476396E-03 2.8444290E-02 at 170iterations 8.9222472E-04 1.6200066E-02 at 180iterations finished qdiffx linear iterations at : 14:59:14 total time elapsed so far: 15.71000 # loops : 180 mean,max change (kT/e) : 8.9222472E-04 1.6200066E-02 energy calculations done at 15.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.85000 DelPhi exited at 14:59:14 15.849u 0.323s 0:17.69 91.3% 0+0k 0+0io 0pf+0w