Tue Oct 11 04:26:03 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 Tue Oct 11 2011 at 04:26:03 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 = 2706 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: 0.6579555 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): -10.78800 37.20800 ymin,ymax (A): -26.20800 22.27400 zmin,zma (A): -8.349000 45.75800 x,y,z range (A): 47.99600 48.48200 54.10700 scale (grids/A): 0.6579555 object centre (A): 13.21000 -1.967000 18.70450 number of atom coordinates read : 2706 total number of charged atoms : 2558 net assigned charge : 2.500024 assigned positive charge : 409.3376 centred at (gu) : 90.00609 90.41871 91.25153 assigned negative charge : -406.8383 centred at (gu) : 89.77466 90.27756 91.26869 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7857 nv = 96 ne = 84 npr = 55192 no. pairs analyzed = 55192 no. exposed pairs = 3307 no. arc points = 23022 no. surface atoms = 1111 nbur = 1595 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 4501 m= 0 mr = 50 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3400000 number of dielectric boundary points 3770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2201 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9311 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2543034E-09 3.3081391E-09 midg,1,midg; midg,igrid,midg -2.0248365E-08 3.6406551E-08 1,midg,midg; igrid,midg,midg -4.0572637E-08 5.0441692E-08 gauss-seidel spectral radius is 0.9880356 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 04:26:04 rms-change max change #iterations 0.1687410 20.63174 at 10iterations 1.8051103E-02 2.438602 at 20iterations 2.0137997E-03 0.2668972 at 30iterations 2.5350656E-04 3.3910751E-02 at 40iterations 4.5470402E-05 6.6375732E-03 at 50iterations finished qdiffx linear iterations at : 04:26:06 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.5470402E-05 6.6375732E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 04:26:07 3.379u 0.152s 0:03.93 89.5% 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 Tue Oct 11 2011 at 04:26:07 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 = 2706 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: 1.973867 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): -10.78800 37.20800 ymin,ymax (A): -26.20800 22.27400 zmin,zma (A): -8.349000 45.75800 x,y,z range (A): 47.99600 48.48200 54.10700 scale (grids/A): 1.973867 object centre (A): 13.21000 -1.967000 18.70450 number of atom coordinates read : 2706 total number of charged atoms : 2558 net assigned charge : 2.500024 assigned positive charge : 409.3376 centred at (gu) : 90.01773 91.25549 93.75414 assigned negative charge : -406.8383 centred at (gu) : 89.32363 90.83241 93.80573 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 85236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23022 grid for indexing accessible points = 1.400000 m= 31970 mr = 60536 m= 5273 mr = 23892 m= 332 mr = 3298 m= 4 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.6700000 number of dielectric boundary points 34963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20211 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) : 0.6579555 object centre at (A) : 13.21000 -1.967000 18.70450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0431427E-02 -1.2168652E-02 midg,1,midg; midg,igrid,midg -1.3202199E-02 2.7995210E-02 1,midg,midg; igrid,midg,midg -1.4726638E-02 6.5861128E-02 gauss-seidel spectral radius is 0.9987381 estimated iterations to convergence 223 setup time was (sec) 0.9400000 now iterating at: 04:26:08 rms-change max change #iterations 4.655922 214.3441 at 10iterations 2.248476 71.19884 at 20iterations 1.086268 34.56909 at 30iterations 0.5236205 16.35415 at 40iterations 0.2536225 8.669015 at 50iterations 0.1224494 3.429698 at 60iterations 5.9237991E-02 1.767517 at 70iterations 2.8558083E-02 0.8472490 at 80iterations 1.3824167E-02 0.3698940 at 90iterations 6.6847689E-03 0.1853480 at 100iterations 3.2513738E-03 0.1040897 at 110iterations 1.5827852E-03 4.7891617E-02 at 120iterations finished qdiffx linear iterations at : 04:26:15 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.5827852E-03 4.7891617E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 04:26:15 7.710u 0.177s 0:08.24 95.6% 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 04:26:16 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 = 2706 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: 2.960800 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): -10.78800 37.20800 ymin,ymax (A): -26.20800 22.27400 zmin,zma (A): -8.349000 45.75800 x,y,z range (A): 47.99600 48.48200 54.10700 scale (grids/A): 2.960800 object centre (A): 13.21000 -1.967000 18.70450 number of atom coordinates read : 2706 total number of charged atoms : 2558 net assigned charge : 2.500024 assigned positive charge : 409.3376 centred at (gu) : 90.02637 91.88303 95.63100 assigned negative charge : -406.8383 centred at (gu) : 88.98547 91.24860 95.70853 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 196946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23022 grid for indexing accessible points = 1.400000 m= 102620 mr = 145892 m= 38104 mr = 85032 m= 9383 mr = 30809 m= 1427 mr = 7018 m= 87 mr = 952 m= 0 mr = 41 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 1422 time to turn everything in is 1.600000 number of dielectric boundary points 78823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 20464 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) : 1.973867 object centre at (A) : 13.21000 -1.967000 18.70450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5828867 0.1634825 midg,1,midg; midg,igrid,midg -0.1568620 0.3489459 1,midg,midg; igrid,midg,midg -9.9056035E-02 0.5603733 gauss-seidel spectral radius is 0.9992820 estimated iterations to convergence 294 setup time was (sec) 1.900000 now iterating at: 04:26:18 rms-change max change #iterations 10.73792 404.6458 at 10iterations 6.302270 129.3635 at 20iterations 3.693283 74.98502 at 30iterations 2.156104 39.13412 at 40iterations 1.260750 23.49203 at 50iterations 0.7368274 13.11886 at 60iterations 0.4294002 7.989086 at 70iterations 0.2496714 4.115953 at 80iterations 0.1452481 2.575324 at 90iterations 8.4470131E-02 1.454094 at 100iterations 4.9201008E-02 0.8085747 at 110iterations 2.8687423E-02 0.5046953 at 120iterations 1.6674830E-02 0.2806392 at 130iterations 9.7366488E-03 0.1737576 at 140iterations 5.6967302E-03 9.9548340E-02 at 150iterations 3.3508912E-03 5.9757233E-02 at 160iterations 1.9939314E-03 3.6354065E-02 at 170iterations 1.2059783E-03 2.3746490E-02 at 180iterations finished qdiffx linear iterations at : 04:26:28 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 1.2059783E-03 2.3746490E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 04:26:29 12.843u 0.181s 0:13.38 97.3% 0+0k 0+0io 0pf+0w