Sat Oct 8 15:52:01 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 8 2011 at 15:52:01 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2294 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.6526362 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): -1.516000 45.59900 ymin,ymax (A): -17.16400 29.20000 zmin,zma (A): -17.74700 36.80100 x,y,z range (A): 47.11500 46.36400 54.54800 scale (grids/A): 0.6526362 object centre (A): 22.04150 6.018000 9.526999 number of atom coordinates read : 2294 total number of charged atoms : 2228 net assigned charge : 2.806002 assigned positive charge : 343.9611 centred at (gu) : 90.54774 88.83927 90.04513 assigned negative charge : -341.1558 centred at (gu) : 90.53561 88.96471 90.10645 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6722 nv = 96 ne = 84 npr = 45716 no. pairs analyzed = 45716 no. exposed pairs = 2900 no. arc points = 20293 no. surface atoms = 986 nbur = 1308 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3726 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1999 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8024 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4208764E-08 -3.2999070E-09 midg,1,midg; midg,igrid,midg 2.9922330E-08 -9.8197939E-09 1,midg,midg; igrid,midg,midg 3.4610408E-09 8.2124467E-09 gauss-seidel spectral radius is 0.9878091 estimated iterations to convergence 74 setup time was (sec) 0.6100000 now iterating at: 15:52:02 rms-change max change #iterations 0.1499248 23.04480 at 10iterations 1.5592830E-02 2.240290 at 20iterations 1.6414112E-03 0.2238693 at 30iterations 1.8669316E-04 2.7679443E-02 at 40iterations 3.0681364E-05 4.3492317E-03 at 50iterations finished qdiffx linear iterations at : 15:52:05 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 3.0681364E-05 4.3492317E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 15:52:06 4.170u 0.282s 0:04.73 94.0% 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 Sat Oct 8 2011 at 15:52:06 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2294 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.957909 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): -1.516000 45.59900 ymin,ymax (A): -17.16400 29.20000 zmin,zma (A): -17.74700 36.80100 x,y,z range (A): 47.11500 46.36400 54.54800 scale (grids/A): 1.957909 object centre (A): 22.04150 6.018000 9.526999 number of atom coordinates read : 2294 total number of charged atoms : 2228 net assigned charge : 2.806002 assigned positive charge : 343.9611 centred at (gu) : 91.64282 86.51727 90.13492 assigned negative charge : -341.1558 centred at (gu) : 91.60655 86.89407 90.31926 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72088 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20293 grid for indexing accessible points = 1.400000 m= 26892 mr = 50160 m= 4746 mr = 20119 m= 345 mr = 3199 m= 7 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 454 time to turn everything in is 0.6600000 number of dielectric boundary points 30452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17584 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) : 0.6526362 object centre at (A) : 22.04150 6.018000 9.526999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6867319E-02 1.0740432E-02 midg,1,midg; midg,igrid,midg 2.4127971E-02 -6.5993401E-03 1,midg,midg; igrid,midg,midg -4.1284170E-03 -4.3819264E-02 gauss-seidel spectral radius is 0.9986790 estimated iterations to convergence 218 setup time was (sec) 0.9600000 now iterating at: 15:52:07 rms-change max change #iterations 4.214854 205.4933 at 10iterations 1.997504 70.76479 at 20iterations 0.9493544 31.42625 at 30iterations 0.4521542 14.15237 at 40iterations 0.2139865 7.043550 at 50iterations 0.1019075 3.336554 at 60iterations 4.8514593E-02 1.621841 at 70iterations 2.2939371E-02 0.7702675 at 80iterations 1.0941937E-02 0.3486488 at 90iterations 5.2036773E-03 0.1673393 at 100iterations 2.4763541E-03 8.1092834E-02 at 110iterations 1.1773222E-03 4.1753769E-02 at 120iterations finished qdiffx linear iterations at : 15:52:16 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 1.1773222E-03 4.1753769E-02 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 15:52:16 9.700u 0.314s 0:10.50 95.3% 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 8 2011 at 15:52:16 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2294 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.936863 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): -1.516000 45.59900 ymin,ymax (A): -17.16400 29.20000 zmin,zma (A): -17.74700 36.80100 x,y,z range (A): 47.11500 46.36400 54.54800 scale (grids/A): 2.936863 object centre (A): 22.04150 6.018000 9.526999 number of atom coordinates read : 2294 total number of charged atoms : 2228 net assigned charge : 2.806002 assigned positive charge : 343.9611 centred at (gu) : 92.46407 84.77570 90.20216 assigned negative charge : -341.1558 centred at (gu) : 92.40980 85.34106 90.47893 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 166568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20293 grid for indexing accessible points = 1.400000 m= 85171 mr = 121516 m= 33045 mr = 69891 m= 8842 mr = 27118 m= 1424 mr = 6944 m= 96 mr = 1012 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1610 time to turn everything in is 1.690000 number of dielectric boundary points 68629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 17822 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) : 1.957909 object centre at (A) : 22.04150 6.018000 9.526999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2791584 0.1095203 midg,1,midg; midg,igrid,midg 0.1806576 -8.3716631E-02 1,midg,midg; igrid,midg,midg -1.2176716E-03 -0.5939693 gauss-seidel spectral radius is 0.9992699 estimated iterations to convergence 292 setup time was (sec) 2.030000 now iterating at: 15:52:19 rms-change max change #iterations 9.857091 505.4485 at 10iterations 5.789330 138.6093 at 20iterations 3.386565 68.59417 at 30iterations 1.982840 38.19236 at 40iterations 1.154359 22.35624 at 50iterations 0.6724496 13.13273 at 60iterations 0.3905362 7.134174 at 70iterations 0.2262251 4.487183 at 80iterations 0.1311457 2.580326 at 90iterations 7.5881653E-02 1.427948 at 100iterations 4.3958895E-02 0.7904873 at 110iterations 2.5361029E-02 0.5011692 at 120iterations 1.4674716E-02 0.2652511 at 130iterations 8.4674703E-03 0.1730261 at 140iterations 4.8959027E-03 9.1999531E-02 at 150iterations 2.8283666E-03 5.2364349E-02 at 160iterations 1.6289287E-03 3.0071259E-02 at 170iterations 9.4170921E-04 1.7060757E-02 at 180iterations finished qdiffx linear iterations at : 15:52:33 total time elapsed so far: 16.19000 # loops : 180 mean,max change (kT/e) : 9.4170921E-04 1.7060757E-02 energy calculations done at 16.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.38000 DelPhi exited at 15:52:33 16.384u 0.331s 0:16.99 98.3% 0+0k 0+0io 0pf+0w