Mon Oct 10 17:16:19 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+sph.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 = amb.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 Mon Oct 10 2011 at 17:16:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5453348 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): -34.95600 17.65500 ymin,ymax (A): -16.79700 31.21800 zmin,zma (A): 10.08700 75.36800 x,y,z range (A): 52.61100 48.01500 65.28101 scale (grids/A): 0.5453348 object centre (A): -8.650500 7.210500 42.72750 number of atom coordinates read : 2905 total number of charged atoms : 2763 net assigned charge : 3.0726194E-05 assigned positive charge : 432.0393 centred at (gu) : 90.49270 91.17136 90.11049 assigned negative charge : -432.0404 centred at (gu) : 90.46477 91.00585 90.06398 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5574 nv = 96 ne = 84 npr = 58175 no. pairs analyzed = 58175 no. exposed pairs = 3760 no. arc points = 26507 no. surface atoms = 1267 nbur = 1638 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 223 mr = 2829 m= 0 mr = 14 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7282 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0029076E-10 2.8508068E-10 midg,1,midg; midg,igrid,midg -8.0440371E-10 1.3558106E-09 1,midg,midg; igrid,midg,midg -1.6840741E-10 1.8270038E-10 gauss-seidel spectral radius is 0.9826590 estimated iterations to convergence 63 setup time was (sec) 0.4000000 now iterating at: 17:16:19 rms-change max change #iterations 7.1728714E-02 13.18477 at 10iterations 4.6844338E-03 1.040604 at 20iterations 3.1257325E-04 5.9164047E-02 at 30iterations 2.0773436E-05 3.4599304E-03 at 40iterations 1.4059862E-06 2.5939941E-04 at 50iterations finished qdiffx linear iterations at : 17:16:22 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.4059862E-06 2.5939941E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 17:16:23 3.418u 0.160s 0:03.92 91.0% 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 Mon Oct 10 2011 at 17:16:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.636004 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): -34.95600 17.65500 ymin,ymax (A): -16.79700 31.21800 zmin,zma (A): 10.08700 75.36800 x,y,z range (A): 52.61100 48.01500 65.28101 scale (grids/A): 1.636004 object centre (A): -8.650500 7.210500 42.72750 number of atom coordinates read : 2905 total number of charged atoms : 2763 net assigned charge : 3.0726194E-05 assigned positive charge : 432.0393 centred at (gu) : 91.47747 93.51330 90.33052 assigned negative charge : -432.0404 centred at (gu) : 91.39408 93.01722 90.19179 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26507 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18296 mr = 41352 m= 1832 mr = 12352 m= 47 mr = 843 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 2107 time to turn everything in is 0.3100000 number of dielectric boundary points 27378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 21145 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) : 0.5453348 object centre at (A) : -8.650500 7.210500 42.72750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4266990E-02 3.1333847E-03 midg,1,midg; midg,igrid,midg -4.8940629E-03 1.0285894E-02 1,midg,midg; igrid,midg,midg -4.9464725E-04 -2.1884330E-03 gauss-seidel spectral radius is 0.9981839 estimated iterations to convergence 186 setup time was (sec) 0.5300000 now iterating at: 17:16:23 rms-change max change #iterations 3.248040 160.4203 at 10iterations 1.346647 51.84401 at 20iterations 0.5600694 21.73658 at 30iterations 0.2338252 9.512772 at 40iterations 9.7788729E-02 3.381073 at 50iterations 4.0640205E-02 1.605760 at 60iterations 1.6921224E-02 0.6388904 at 70iterations 7.0639965E-03 0.2616825 at 80iterations 2.9399409E-03 9.8509312E-02 at 90iterations 1.2299148E-03 5.1324844E-02 at 100iterations 5.1185355E-04 1.8642426E-02 at 110iterations 2.1399309E-04 8.1543922E-03 at 120iterations finished qdiffx linear iterations at : 17:16:30 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 2.1399309E-04 8.1543922E-03 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 17:16:31 7.680u 0.192s 0:08.24 95.5% 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 Mon Oct 10 2011 at 17:16:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.454006 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): -34.95600 17.65500 ymin,ymax (A): -16.79700 31.21800 zmin,zma (A): 10.08700 75.36800 x,y,z range (A): 52.61100 48.01500 65.28101 scale (grids/A): 2.454006 object centre (A): -8.650500 7.210500 42.72750 number of atom coordinates read : 2905 total number of charged atoms : 2763 net assigned charge : 3.0726194E-05 assigned positive charge : 432.0393 centred at (gu) : 92.21587 95.26980 90.49570 assigned negative charge : -432.0404 centred at (gu) : 92.09088 94.52583 90.28760 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 143301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26507 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 64014 mr = 101070 m= 17594 mr = 50111 m= 2933 mr = 13049 m= 210 mr = 1902 m= 2 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 7247 time to turn everything in is 0.7400000 number of dielectric boundary points 61822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 22078 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) : 1.636004 object centre at (A) : -8.650500 7.210500 42.72750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2561593 0.1426722 midg,1,midg; midg,igrid,midg -6.0860664E-02 0.1177482 1,midg,midg; igrid,midg,midg -2.1400696E-02 -1.9563367E-03 gauss-seidel spectral radius is 0.9991363 estimated iterations to convergence 269 setup time was (sec) 0.9700000 now iterating at: 17:16:32 rms-change max change #iterations 8.397489 350.1873 at 10iterations 4.672579 132.3211 at 20iterations 2.598815 62.47465 at 30iterations 1.439645 35.10370 at 40iterations 0.7942293 18.11573 at 50iterations 0.4385310 9.560049 at 60iterations 0.2405488 5.257460 at 70iterations 0.1328120 2.776402 at 80iterations 7.3038325E-02 1.773884 at 90iterations 4.0056594E-02 0.8517227 at 100iterations 2.1983560E-02 0.5285926 at 110iterations 1.2107165E-02 0.2509232 at 120iterations 6.6590244E-03 0.1553230 at 130iterations 3.6652407E-03 8.3797455E-02 at 140iterations 2.0205865E-03 4.7969818E-02 at 150iterations 1.1172710E-03 2.8312683E-02 at 160iterations 6.2490045E-04 1.6075134E-02 at 170iterations 3.5381663E-04 1.0035515E-02 at 180iterations finished qdiffx linear iterations at : 17:16:43 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 3.5381663E-04 1.0035515E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 17:16:44 12.191u 0.195s 0:12.82 96.5% 0+0k 0+0io 0pf+0w