Sun Oct 9 09:04:32 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+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 Sun Oct 9 2011 at 09:04:32 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: 223 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 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: 0.5807315 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 0.5807315 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2781 total number of charged atoms : 2651 net assigned charge : -0.4999969 assigned positive charge : 379.1896 centred at (gu) : 91.98788 90.39842 89.99960 assigned negative charge : -379.6906 centred at (gu) : 91.97378 90.25903 89.99861 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6323 nv = 96 ne = 84 npr = 57446 no. pairs analyzed = 57446 no. exposed pairs = 3568 no. arc points = 25516 no. surface atoms = 1212 nbur = 1569 mkacc time = 0.1200000 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 = 1.456000 m= 311 mr = 3165 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2474 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7900 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4669796E-10 -1.0868275E-10 midg,1,midg; midg,igrid,midg -2.5896660E-09 2.7522895E-09 1,midg,midg; igrid,midg,midg -2.5129443E-10 2.3411420E-10 gauss-seidel spectral radius is 0.9846916 estimated iterations to convergence 66 setup time was (sec) 0.5200000 now iterating at: 09:04:32 rms-change max change #iterations 9.1469832E-02 14.97543 at 10iterations 8.5928971E-03 1.418480 at 20iterations 2.4056858E-03 0.4618416 at 30iterations 1.0975660E-03 0.2168808 at 40iterations 5.1525241E-04 0.1016159 at 50iterations finished qdiffx linear iterations at : 09:04:35 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 5.1525241E-04 0.1016159 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 09:04:35 3.125u 0.139s 0:03.53 92.0% 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 Sun Oct 9 2011 at 09:04:35 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: 223 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 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: 1.742194 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 1.742194 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2781 total number of charged atoms : 2651 net assigned charge : -0.4999969 assigned positive charge : 379.1896 centred at (gu) : 95.96297 91.19487 89.99844 assigned negative charge : -379.6906 centred at (gu) : 95.92087 90.77683 89.99566 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25516 grid for indexing accessible points = 1.400000 m= 23400 mr = 45498 m= 3499 mr = 16355 m= 133 mr = 2112 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 31904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 20616 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) : 0.5807315 object centre at (A) : -1.655001 -10.39300 4.592001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5130973E-03 -6.3820565E-03 midg,1,midg; midg,igrid,midg -6.7758327E-03 1.1612416E-02 1,midg,midg; igrid,midg,midg 9.4306550E-04 4.9486110E-04 gauss-seidel spectral radius is 0.9984004 estimated iterations to convergence 198 setup time was (sec) 0.8100000 now iterating at: 09:04:36 rms-change max change #iterations 3.475559 142.6703 at 10iterations 1.518814 60.38420 at 20iterations 0.6670701 24.41983 at 30iterations 0.2946360 10.10701 at 40iterations 0.1297727 4.373491 at 50iterations 5.7369675E-02 1.909181 at 60iterations 2.5970878E-02 0.8395481 at 70iterations 1.2284152E-02 0.4733009 at 80iterations 6.4487071E-03 0.2527008 at 90iterations 3.9341976E-03 0.1699104 at 100iterations 2.7160528E-03 0.1060600 at 110iterations 2.0114800E-03 7.9040527E-02 at 120iterations finished qdiffx linear iterations at : 09:04:43 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 2.0114800E-03 7.9040527E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 09:04:43 7.703u 0.198s 0:08.22 95.9% 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 Sun Oct 9 2011 at 09:04:43 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: 223 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.613292 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 2.613292 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2781 total number of charged atoms : 2651 net assigned charge : -0.4999969 assigned positive charge : 379.1896 centred at (gu) : 98.94427 91.79211 89.99741 assigned negative charge : -379.6906 centred at (gu) : 98.88136 91.16518 89.99345 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 159619 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25516 grid for indexing accessible points = 1.400000 m= 75959 mr = 111687 m= 27314 mr = 59771 m= 6107 mr = 21257 m= 614 mr = 4471 m= 12 mr = 378 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 72061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 21200 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) : 1.742194 object centre at (A) : -1.655001 -10.39300 4.592001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1334546 -0.1017937 midg,1,midg; midg,igrid,midg -9.9107437E-03 9.5846027E-02 1,midg,midg; igrid,midg,midg 8.8968277E-03 -7.8882147E-03 gauss-seidel spectral radius is 0.9992032 estimated iterations to convergence 280 setup time was (sec) 1.540000 now iterating at: 09:04:45 rms-change max change #iterations 8.686650 277.8020 at 10iterations 5.007100 126.5395 at 20iterations 2.885379 63.19955 at 30iterations 1.646367 34.94710 at 40iterations 0.9379685 19.63195 at 50iterations 0.5326778 10.84345 at 60iterations 0.3017733 6.134211 at 70iterations 0.1709256 3.221466 at 80iterations 9.6601099E-02 2.218468 at 90iterations 5.4684050E-02 1.023250 at 100iterations 3.0975362E-02 0.6853638 at 110iterations 1.7609598E-02 0.3635826 at 120iterations 1.0131147E-02 0.2179832 at 130iterations 5.9673525E-03 0.1419067 at 140iterations 3.6705260E-03 8.5819244E-02 at 150iterations 2.4191639E-03 5.9978485E-02 at 160iterations 1.7367658E-03 4.0649414E-02 at 170iterations 1.3427355E-03 3.0353546E-02 at 180iterations finished qdiffx linear iterations at : 09:04:56 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 1.3427355E-03 3.0353546E-02 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 09:04:56 12.210u 0.241s 0:12.73 97.8% 0+0k 0+0io 0pf+0w