Sun Oct 9 06:22:08 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 06:22:08 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1988 !!! WARNING: ASP 186 has a net charge of -0.2720 !!! WARNING: NDP 202 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7369837 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): -3.291000 39.19300 ymin,ymax (A): 5.689000 46.83300 zmin,zma (A): 8.419000 56.72400 x,y,z range (A): 42.48400 41.14400 48.30500 scale (grids/A): 0.7369837 object centre (A): 17.95100 26.26100 32.57150 number of atom coordinates read : 1988 total number of charged atoms : 1847 net assigned charge : -0.7719850 assigned positive charge : 297.5060 centred at (gu) : 90.66505 89.70256 90.31401 assigned negative charge : -298.2781 centred at (gu) : 90.73618 89.79864 90.14298 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7419 nv = 96 ne = 84 npr = 41932 no. pairs analyzed = 41932 no. exposed pairs = 2391 no. arc points = 17013 no. surface atoms = 802 nbur = 1186 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 511 mr = 4269 m= 3 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 58 time to turn everything in is 0.2700000 number of dielectric boundary points 3553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1482 ## 117 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7885 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5783827E-07 1.4545913E-07 midg,1,midg; midg,igrid,midg 7.6143863E-08 -9.3701580E-08 1,midg,midg; igrid,midg,midg 4.3923539E-08 -8.7027054E-08 gauss-seidel spectral radius is 0.9903916 estimated iterations to convergence 83 setup time was (sec) 0.5100000 now iterating at: 06:22:09 rms-change max change #iterations 0.2328063 34.98349 at 10iterations 3.1775359E-02 4.562408 at 20iterations 4.2130779E-03 0.5065298 at 30iterations 5.6371186E-04 7.6007843E-02 at 40iterations 7.5001190E-05 1.0487556E-02 at 50iterations finished qdiffx linear iterations at : 06:22:11 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.5001190E-05 1.0487556E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 06:22:12 3.435u 0.222s 0:03.96 92.1% 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 06:22:12 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1988 !!! WARNING: ASP 186 has a net charge of -0.2720 !!! WARNING: NDP 202 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.210951 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): -3.291000 39.19300 ymin,ymax (A): 5.689000 46.83300 zmin,zma (A): 8.419000 56.72400 x,y,z range (A): 42.48400 41.14400 48.30500 scale (grids/A): 2.210951 object centre (A): 17.95100 26.26100 32.57150 number of atom coordinates read : 1988 total number of charged atoms : 1847 net assigned charge : -0.7719850 assigned positive charge : 297.5060 centred at (gu) : 91.99510 89.10750 90.94201 assigned negative charge : -298.2781 centred at (gu) : 92.20848 89.39610 90.42896 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78537 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17013 grid for indexing accessible points = 1.400000 m= 31168 mr = 55368 m= 6640 mr = 23950 m= 690 mr = 4747 m= 42 mr = 346 m= 0 mr = 13 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1982 time to turn everything in is 0.5800000 number of dielectric boundary points 32653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 14726 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) : 0.7369837 object centre at (A) : 17.95100 26.26100 32.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0560385E-02 8.5545722E-03 midg,1,midg; midg,igrid,midg 2.5772141E-02 6.9720196E-03 1,midg,midg; igrid,midg,midg -2.0530098E-03 -1.6102217E-02 gauss-seidel spectral radius is 0.9989067 estimated iterations to convergence 239 setup time was (sec) 0.8800000 now iterating at: 06:22:13 rms-change max change #iterations 4.918243 194.9234 at 10iterations 2.491987 81.28927 at 20iterations 1.260633 41.12289 at 30iterations 0.6441825 19.39254 at 40iterations 0.3256239 9.692488 at 50iterations 0.1650252 4.973724 at 60iterations 8.3913840E-02 2.659210 at 70iterations 4.2627398E-02 1.205559 at 80iterations 2.1558741E-02 0.6598115 at 90iterations 1.0947397E-02 0.3352356 at 100iterations 5.5578812E-03 0.1600952 at 110iterations 2.8107888E-03 7.6251984E-02 at 120iterations finished qdiffx linear iterations at : 06:22:20 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.8107888E-03 7.6251984E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 06:22:20 7.954u 0.267s 0:08.60 95.4% 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 06:22:21 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1988 !!! WARNING: ASP 186 has a net charge of -0.2720 !!! WARNING: NDP 202 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: 3.316427 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): -3.291000 39.19300 ymin,ymax (A): 5.689000 46.83300 zmin,zma (A): 8.419000 56.72400 x,y,z range (A): 42.48400 41.14400 48.30500 scale (grids/A): 3.316427 object centre (A): 17.95100 26.26100 32.57150 number of atom coordinates read : 1988 total number of charged atoms : 1847 net assigned charge : -0.7719850 assigned positive charge : 297.5060 centred at (gu) : 92.99269 88.66147 91.41312 assigned negative charge : -298.2781 centred at (gu) : 93.31271 89.09413 90.64342 start vw surface at 0.1400000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 180672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17013 grid for indexing accessible points = 1.400000 m= 96709 mr = 132719 m= 40232 mr = 81102 m= 12894 mr = 33630 m= 2815 mr = 10357 m= 419 mr = 2069 m= 40 mr = 271 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 7097 time to turn everything in is 1.830000 number of dielectric boundary points 73606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 14772 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) : 2.210951 object centre at (A) : 17.95100 26.26100 32.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2937505 0.1346847 midg,1,midg; midg,igrid,midg 0.3403564 4.7756962E-02 1,midg,midg; igrid,midg,midg -5.8379620E-02 -0.1000677 gauss-seidel spectral radius is 0.9993057 estimated iterations to convergence 299 setup time was (sec) 2.160000 now iterating at: 06:22:23 rms-change max change #iterations 10.53773 307.4470 at 10iterations 6.132408 119.7599 at 20iterations 3.581238 64.07189 at 30iterations 2.088171 36.25740 at 40iterations 1.220396 20.29310 at 50iterations 0.7126155 12.58401 at 60iterations 0.4156001 6.959596 at 70iterations 0.2428485 4.084610 at 80iterations 0.1414292 2.311861 at 90iterations 8.2649551E-02 1.575009 at 100iterations 4.8170641E-02 0.7428589 at 110iterations 2.8195143E-02 0.4450035 at 120iterations 1.6461030E-02 0.2719269 at 130iterations 9.6113784E-03 0.1546173 at 140iterations 5.5960459E-03 0.1024971 at 150iterations 3.2790455E-03 5.5798531E-02 at 160iterations 1.9149149E-03 3.5396576E-02 at 170iterations 1.1187326E-03 1.8870354E-02 at 180iterations finished qdiffx linear iterations at : 06:22:34 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 1.1187326E-03 1.8870354E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 06:22:34 13.243u 0.276s 0:13.93 96.9% 0+0k 0+0io 0pf+0w