Sun Oct 9 06:12:54 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 Sun Oct 9 2011 at 06:12:55 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1997 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 0.6598948 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): 2.055000 44.33600 ymin,ymax (A): -8.868000 38.14500 zmin,zma (A): -24.20500 29.74300 x,y,z range (A): 42.28100 47.01300 53.94800 scale (grids/A): 0.6598948 object centre (A): 23.19550 14.63850 2.769000 number of atom coordinates read : 1997 total number of charged atoms : 1858 net assigned charge : -2.499987 assigned positive charge : 301.6950 centred at (gu) : 89.99479 89.11284 88.06427 assigned negative charge : -304.1951 centred at (gu) : 89.83711 88.93179 88.01492 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5844 nv = 96 ne = 84 npr = 42049 no. pairs analyzed = 42049 no. exposed pairs = 2440 no. arc points = 17479 no. surface atoms = 814 nbur = 1183 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3237 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2400000 number of dielectric boundary points 2866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1662 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6792 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0163117E-08 1.0640833E-09 midg,1,midg; midg,igrid,midg -4.1269097E-08 1.7784327E-08 1,midg,midg; igrid,midg,midg -3.0511977E-08 1.8022005E-08 gauss-seidel spectral radius is 0.9880416 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 06:12:55 rms-change max change #iterations 0.1543473 28.60525 at 10iterations 1.6228503E-02 2.598083 at 20iterations 1.6989129E-03 0.2450829 at 30iterations 1.8245682E-04 2.8278351E-02 at 40iterations 1.8964995E-05 2.9640198E-03 at 50iterations finished qdiffx linear iterations at : 06:12:58 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 1.8964995E-05 2.9640198E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 06:12:58 3.154u 0.166s 0:03.63 91.1% 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 Sun Oct 9 2011 at 06:12:58 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1997 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 1.979684 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): 2.055000 44.33600 ymin,ymax (A): -8.868000 38.14500 zmin,zma (A): -24.20500 29.74300 x,y,z range (A): 42.28100 47.01300 53.94800 scale (grids/A): 1.979684 object centre (A): 23.19550 14.63850 2.769000 number of atom coordinates read : 1997 total number of charged atoms : 1858 net assigned charge : -2.499987 assigned positive charge : 301.6950 centred at (gu) : 89.98450 87.33855 84.19293 assigned negative charge : -304.1951 centred at (gu) : 89.51120 86.79553 84.04493 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17479 grid for indexing accessible points = 1.400000 m= 23284 mr = 42833 m= 4101 mr = 17604 m= 285 mr = 2800 m= 5 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2650 time to turn everything in is 0.4700000 number of dielectric boundary points 26401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14680 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) : 0.6598948 object centre at (A) : 23.19550 14.63850 2.769000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0449934E-02 2.4805132E-02 midg,1,midg; midg,igrid,midg -2.6233682E-02 1.3854042E-02 1,midg,midg; igrid,midg,midg -3.3076264E-02 7.7568977E-03 gauss-seidel spectral radius is 0.9986671 estimated iterations to convergence 217 setup time was (sec) 0.7400000 now iterating at: 06:12:59 rms-change max change #iterations 4.097586 215.3163 at 10iterations 1.925546 74.05901 at 20iterations 0.9065452 29.92772 at 30iterations 0.4296846 14.66155 at 40iterations 0.2024899 6.932492 at 50iterations 9.5704600E-02 3.067883 at 60iterations 4.5287669E-02 1.593723 at 70iterations 2.1317633E-02 0.6672645 at 80iterations 1.0083745E-02 0.3385401 at 90iterations 4.7767246E-03 0.1596413 at 100iterations 2.2585739E-03 7.8346252E-02 at 110iterations 1.0670624E-03 3.9199829E-02 at 120iterations finished qdiffx linear iterations at : 06:13:05 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 1.0670624E-03 3.9199829E-02 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 06:13:06 7.235u 0.198s 0:07.71 96.2% 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 Sun Oct 9 2011 at 06:13:06 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1997 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.969526 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): 2.055000 44.33600 ymin,ymax (A): -8.868000 38.14500 zmin,zma (A): -24.20500 29.74300 x,y,z range (A): 42.28100 47.01300 53.94800 scale (grids/A): 2.969526 object centre (A): 23.19550 14.63850 2.769000 number of atom coordinates read : 1997 total number of charged atoms : 1858 net assigned charge : -2.499987 assigned positive charge : 301.6950 centred at (gu) : 89.97672 86.00784 81.28941 assigned negative charge : -304.1951 centred at (gu) : 89.26683 85.19339 81.06738 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 143233 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17479 grid for indexing accessible points = 1.400000 m= 73487 mr = 103127 m= 28381 mr = 60939 m= 7675 mr = 23563 m= 1316 mr = 6073 m= 86 mr = 922 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 8965 time to turn everything in is 1.150000 number of dielectric boundary points 59517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14864 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) : 1.979684 object centre at (A) : 23.19550 14.63850 2.769000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6579340 0.6186041 midg,1,midg; midg,igrid,midg -0.1807617 0.1843215 1,midg,midg; igrid,midg,midg -0.3249690 2.8556561E-02 gauss-seidel spectral radius is 0.9992517 estimated iterations to convergence 289 setup time was (sec) 1.420000 now iterating at: 06:13:08 rms-change max change #iterations 9.375714 430.1876 at 10iterations 5.390186 154.3979 at 20iterations 3.090400 72.20235 at 30iterations 1.774288 38.77996 at 40iterations 1.019048 21.63958 at 50iterations 0.5853250 11.93512 at 60iterations 0.3343818 7.342674 at 70iterations 0.1916360 4.039101 at 80iterations 0.1095006 2.127050 at 90iterations 6.2928848E-02 1.353495 at 100iterations 3.5927642E-02 0.7785034 at 110iterations 2.0540541E-02 0.3811188 at 120iterations 1.1775924E-02 0.2414031 at 130iterations 6.7286822E-03 0.1287804 at 140iterations 3.8592634E-03 9.3488693E-02 at 150iterations 2.2085307E-03 4.5609474E-02 at 160iterations 1.2617437E-03 2.3544312E-02 at 170iterations 7.2439242E-04 1.3644218E-02 at 180iterations finished qdiffx linear iterations at : 06:13:18 total time elapsed so far: 11.62000 # loops : 180 mean,max change (kT/e) : 7.2439242E-04 1.3644218E-02 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.80000 DelPhi exited at 06:13:18 11.806u 0.192s 0:12.27 97.7% 0+0k 0+0io 0pf+0w