Mon Oct 10 17:02:38 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 17:02:38 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7473809 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): 34.63600 82.26900 ymin,ymax (A): 10.92200 52.35900 zmin,zma (A): 25.47000 60.31000 x,y,z range (A): 47.63301 41.43700 34.84000 scale (grids/A): 0.7473809 object centre (A): 58.45250 31.64050 42.89000 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 90.33264 90.32694 88.56726 assigned negative charge : -192.8082 centred at (gu) : 90.47347 90.25440 88.51639 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4853 nv = 96 ne = 84 npr = 27495 no. pairs analyzed = 27495 no. exposed pairs = 1636 no. arc points = 12008 no. surface atoms = 559 nbur = 802 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 2532 m= 5 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 2605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1047 ## 99 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 5160 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8021994E-07 2.8400461E-07 midg,1,midg; midg,igrid,midg 2.6329559E-07 4.0492384E-07 1,midg,midg; igrid,midg,midg 4.0412442E-07 2.4310569E-07 gauss-seidel spectral radius is 0.9905851 estimated iterations to convergence 84 setup time was (sec) 0.3100000 now iterating at: 17:02:39 rms-change max change #iterations 0.1966917 31.62576 at 10iterations 2.6323084E-02 4.091572 at 20iterations 3.5821069E-03 0.7830558 at 30iterations 4.7622863E-04 7.7672958E-02 at 40iterations 6.6102679E-05 9.9868774E-03 at 50iterations finished qdiffx linear iterations at : 17:02:41 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 6.6102679E-05 9.9868774E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 17:02:42 3.279u 0.176s 0:04.18 82.2% 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 Mon Oct 10 2011 at 17:02:42 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.242143 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): 34.63600 82.26900 ymin,ymax (A): 10.92200 52.35900 zmin,zma (A): 25.47000 60.31000 x,y,z range (A): 47.63301 41.43700 34.84000 scale (grids/A): 2.242143 object centre (A): 58.45250 31.64050 42.89000 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 90.99825 90.98104 85.70201 assigned negative charge : -192.8082 centred at (gu) : 91.42059 90.76341 85.54929 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 51000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12008 grid for indexing accessible points = 1.400000 m= 19117 mr = 33779 m= 4152 mr = 13976 m= 509 mr = 2737 m= 29 mr = 287 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 24016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9869 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) : 0.7473809 object centre at (A) : 58.45250 31.64050 42.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2938644E-02 3.0125029E-02 midg,1,midg; midg,igrid,midg 3.0902309E-02 8.9198828E-02 1,midg,midg; igrid,midg,midg 0.1325396 0.1005453 gauss-seidel spectral radius is 0.9988627 estimated iterations to convergence 235 setup time was (sec) 0.4900000 now iterating at: 17:02:43 rms-change max change #iterations 3.907747 186.8334 at 10iterations 1.945875 78.24641 at 20iterations 0.9711611 36.55795 at 30iterations 0.4841788 17.60772 at 40iterations 0.2408199 8.456406 at 50iterations 0.1214204 4.235703 at 60iterations 6.0438219E-02 2.226501 at 70iterations 3.0156234E-02 1.154950 at 80iterations 1.5047923E-02 0.5271692 at 90iterations 7.5178044E-03 0.2591572 at 100iterations 3.7630822E-03 0.1376438 at 110iterations 1.8738641E-03 6.4026356E-02 at 120iterations finished qdiffx linear iterations at : 17:02:50 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.8738641E-03 6.4026356E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 17:02:52 7.773u 0.222s 0:09.54 83.7% 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 17:02:53 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.363214 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): 34.63600 82.26900 ymin,ymax (A): 10.92200 52.35900 zmin,zma (A): 25.47000 60.31000 x,y,z range (A): 47.63301 41.43700 34.84000 scale (grids/A): 3.363214 object centre (A): 58.45250 31.64050 42.89000 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 91.49738 91.47149 83.55318 assigned negative charge : -192.8082 centred at (gu) : 92.13094 91.14510 83.32396 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 117454 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12008 grid for indexing accessible points = 1.400000 m= 58757 mr = 81786 m= 24547 mr = 47443 m= 7889 mr = 19798 m= 1985 mr = 6048 m= 331 mr = 1477 m= 31 mr = 243 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 54185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 9904 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) : 2.242143 object centre at (A) : 58.45250 31.64050 42.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3552167 0.1651998 midg,1,midg; midg,igrid,midg 0.1633570 0.7360973 1,midg,midg; igrid,midg,midg 1.033610 0.7962855 gauss-seidel spectral radius is 0.9992981 estimated iterations to convergence 298 setup time was (sec) 1.140000 now iterating at: 17:02:54 rms-change max change #iterations 8.582611 370.0295 at 10iterations 5.021150 114.8027 at 20iterations 2.932092 63.66801 at 30iterations 1.713906 40.67506 at 40iterations 0.9979004 21.06606 at 50iterations 0.5811965 11.19951 at 60iterations 0.3389811 6.657914 at 70iterations 0.1967628 4.233658 at 80iterations 0.1147120 2.366866 at 90iterations 6.6717707E-02 1.457726 at 100iterations 3.8805861E-02 0.8153670 at 110iterations 2.2582557E-02 0.4317055 at 120iterations 1.3121286E-02 0.2825775 at 130iterations 7.6637785E-03 0.1429808 at 140iterations 4.4528875E-03 9.3849182E-02 at 150iterations 2.5860842E-03 5.4393768E-02 at 160iterations 1.5059357E-03 2.9781342E-02 at 170iterations 8.7722408E-04 1.8468857E-02 at 180iterations finished qdiffx linear iterations at : 17:03:06 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 8.7722408E-04 1.8468857E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 17:03:06 12.898u 0.262s 0:13.45 97.7% 0+0k 0+0io 0pf+0w