Tue Oct 11 08:39:32 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 08:39:32 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7092764 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): -5.226000 44.96600 ymin,ymax (A): 38.75000 85.47100 zmin,zma (A): -13.53200 28.37800 x,y,z range (A): 50.19200 46.72100 41.91000 scale (grids/A): 0.7092764 object centre (A): 19.87000 62.11050 7.423000 number of atom coordinates read : 2049 total number of charged atoms : 1919 net assigned charge : 6.039010 assigned positive charge : 312.9611 centred at (gu) : 90.91673 91.04309 90.37167 assigned negative charge : -306.9221 centred at (gu) : 90.84126 90.94497 90.42656 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6921 nv = 96 ne = 84 npr = 41280 no. pairs analyzed = 41280 no. exposed pairs = 2466 no. arc points = 16862 no. surface atoms = 841 nbur = 1208 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4008 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1597 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7754 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4451805E-08 2.5997377E-08 midg,1,midg; midg,igrid,midg 2.2978626E-09 1.2426590E-07 1,midg,midg; igrid,midg,midg 1.2011586E-08 1.0769956E-07 gauss-seidel spectral radius is 0.9896339 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 08:39:33 rms-change max change #iterations 0.2030466 28.51815 at 10iterations 2.5454447E-02 3.514248 at 20iterations 3.5644784E-03 0.4620056 at 30iterations 6.3115224E-04 8.3566666E-02 at 40iterations 1.6635444E-04 2.2914886E-02 at 50iterations finished qdiffx linear iterations at : 08:39:35 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.6635444E-04 2.2914886E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 08:39:36 3.313u 0.168s 0:03.95 87.8% 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 Tue Oct 11 2011 at 08:39:36 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.127829 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): -5.226000 44.96600 ymin,ymax (A): 38.75000 85.47100 zmin,zma (A): -13.53200 28.37800 x,y,z range (A): 50.19200 46.72100 41.91000 scale (grids/A): 2.127829 object centre (A): 19.87000 62.11050 7.423000 number of atom coordinates read : 2049 total number of charged atoms : 1919 net assigned charge : 6.039010 assigned positive charge : 312.9611 centred at (gu) : 92.75017 93.12960 91.11517 assigned negative charge : -306.9221 centred at (gu) : 92.52399 92.83510 91.27970 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 74188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 29441 mr = 52964 m= 5459 mr = 22226 m= 465 mr = 3555 m= 18 mr = 251 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 0.3600000 number of dielectric boundary points 30575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15238 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) : 0.7092764 object centre at (A) : 19.87000 62.11050 7.423000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4401508E-02 2.5098924E-02 midg,1,midg; midg,igrid,midg -4.7425926E-02 3.3104889E-02 1,midg,midg; igrid,midg,midg 5.7130735E-02 4.8239712E-02 gauss-seidel spectral radius is 0.9988322 estimated iterations to convergence 232 setup time was (sec) 0.5700000 now iterating at: 08:39:37 rms-change max change #iterations 4.622841 198.5844 at 10iterations 2.287869 72.86548 at 20iterations 1.136183 35.72027 at 30iterations 0.5646626 16.76173 at 40iterations 0.2790433 8.081122 at 50iterations 0.1389442 4.324012 at 60iterations 6.9355436E-02 2.202185 at 70iterations 3.4512661E-02 1.007233 at 80iterations 1.7298931E-02 0.5121143 at 90iterations 8.7198680E-03 0.2535934 at 100iterations 4.4103279E-03 0.1354179 at 110iterations 2.2776213E-03 7.2456360E-02 at 120iterations finished qdiffx linear iterations at : 08:39:44 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 2.2776213E-03 7.2456360E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 08:39:45 7.680u 0.198s 0:08.56 91.9% 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 08:39:45 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.191744 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): -5.226000 44.96600 ymin,ymax (A): 38.75000 85.47100 zmin,zma (A): -13.53200 28.37800 x,y,z range (A): 50.19200 46.72100 41.91000 scale (grids/A): 3.191744 object centre (A): 19.87000 62.11050 7.423000 number of atom coordinates read : 2049 total number of charged atoms : 1919 net assigned charge : 6.039010 assigned positive charge : 312.9611 centred at (gu) : 94.12531 94.69447 91.67274 assigned negative charge : -306.9221 centred at (gu) : 93.78593 94.25256 91.91966 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 171356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 92447 mr = 127694 m= 36965 mr = 76955 m= 10190 mr = 30147 m= 1973 mr = 7861 m= 266 mr = 1412 m= 7 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 68970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 15352 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) : 2.127829 object centre at (A) : 19.87000 62.11050 7.423000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1019046E-02 0.1806943 midg,1,midg; midg,igrid,midg -0.5065954 0.2722018 1,midg,midg; igrid,midg,midg 0.4584820 0.3633187 gauss-seidel spectral radius is 0.9992964 estimated iterations to convergence 297 setup time was (sec) 1.380000 now iterating at: 08:39:46 rms-change max change #iterations 10.25378 423.4864 at 10iterations 6.043387 131.3115 at 20iterations 3.557159 67.91983 at 30iterations 2.090477 46.77897 at 40iterations 1.225433 23.49368 at 50iterations 0.7194713 13.41682 at 60iterations 0.4227422 7.925636 at 70iterations 0.2471634 4.613627 at 80iterations 0.1447132 2.723511 at 90iterations 8.4942073E-02 1.896854 at 100iterations 4.9961261E-02 1.023201 at 110iterations 2.9466512E-02 0.4898453 at 120iterations 1.7501734E-02 0.3463898 at 130iterations 1.0588258E-02 0.1927605 at 140iterations 6.5865568E-03 0.1330109 at 150iterations 4.2366260E-03 8.2071304E-02 at 160iterations 2.8966316E-03 5.7334900E-02 at 170iterations 2.0829067E-03 4.1839600E-02 at 180iterations finished qdiffx linear iterations at : 08:39:57 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 2.0829067E-03 4.1839600E-02 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 08:39:58 12.584u 0.191s 0:13.15 97.1% 0+0k 0+0io 0pf+0w