Tue Oct 11 01:13:02 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 01:13:02 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 = 2623 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 0.5925334 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): -34.14900 19.69500 ymin,ymax (A): 15.45300 75.53400 zmin,zma (A): 16.90200 60.10100 x,y,z range (A): 53.84400 60.08100 43.19900 scale (grids/A): 0.5925334 object centre (A): -7.227001 45.49350 38.50150 number of atom coordinates read : 2623 total number of charged atoms : 2481 net assigned charge : 3.500015 assigned positive charge : 393.5078 centred at (gu) : 89.22516 90.30907 90.25555 assigned negative charge : -390.0085 centred at (gu) : 89.22110 90.58795 90.08253 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6040 nv = 96 ne = 84 npr = 53327 no. pairs analyzed = 53327 no. exposed pairs = 3079 no. arc points = 21741 no. surface atoms = 1047 nbur = 1576 mkacc time = 0.1400000 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= 258 mr = 3356 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3000000 number of dielectric boundary points 2921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2173 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7596 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6860051E-09 6.4949846E-09 midg,1,midg; midg,igrid,midg 8.4097227E-09 -7.6969373E-09 1,midg,midg; igrid,midg,midg 1.2902615E-09 1.1123723E-09 gauss-seidel spectral radius is 0.9852607 estimated iterations to convergence 68 setup time was (sec) 0.5700000 now iterating at: 01:13:03 rms-change max change #iterations 0.1024178 20.06459 at 10iterations 9.1151418E-03 1.509338 at 20iterations 1.1871075E-03 0.2668533 at 30iterations 2.8459099E-04 7.1319580E-02 at 40iterations 7.6134223E-05 1.9695282E-02 at 50iterations finished qdiffx linear iterations at : 01:13:07 total time elapsed so far: 4.680000 # loops : 50 mean,max change (kT/e) : 7.6134223E-05 1.9695282E-02 energy calculations done at 4.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 01:13:07 4.864u 0.367s 0:05.55 94.0% 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 Tue Oct 11 2011 at 01:13:07 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 = 2623 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.777600 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): -34.14900 19.69500 ymin,ymax (A): 15.45300 75.53400 zmin,zma (A): 16.90200 60.10100 x,y,z range (A): 53.84400 60.08100 43.19900 scale (grids/A): 1.777600 object centre (A): -7.227001 45.49350 38.50150 number of atom coordinates read : 2623 total number of charged atoms : 2481 net assigned charge : 3.500015 assigned positive charge : 393.5078 centred at (gu) : 87.67464 90.92674 90.76594 assigned negative charge : -390.0085 centred at (gu) : 87.66309 91.76365 90.24734 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21741 grid for indexing accessible points = 1.400000 m= 21949 mr = 46963 m= 2771 mr = 16051 m= 90 mr = 1639 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1264 time to turn everything in is 0.5600000 number of dielectric boundary points 26921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19350 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) : 0.5925334 object centre at (A) : -7.227001 45.49350 38.50150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6978271E-03 2.4286337E-02 midg,1,midg; midg,igrid,midg -1.0035174E-02 -6.5787837E-02 1,midg,midg; igrid,midg,midg 9.7486452E-04 6.6593504E-03 gauss-seidel spectral radius is 0.9984346 estimated iterations to convergence 201 setup time was (sec) 0.9000000 now iterating at: 01:13:09 rms-change max change #iterations 3.655321 166.3788 at 10iterations 1.618310 71.11723 at 20iterations 0.7193930 29.07657 at 30iterations 0.3194191 11.71553 at 40iterations 0.1423517 4.797143 at 50iterations 6.3418992E-02 2.110723 at 60iterations 2.8091466E-02 0.9740486 at 70iterations 1.2635522E-02 0.4277496 at 80iterations 5.6992518E-03 0.2019043 at 90iterations 2.6223094E-03 9.4932556E-02 at 100iterations 1.2562269E-03 4.6890259E-02 at 110iterations 6.2830711E-04 2.6088715E-02 at 120iterations finished qdiffx linear iterations at : 01:13:19 total time elapsed so far: 11.11000 # loops : 120 mean,max change (kT/e) : 6.2830711E-04 2.6088715E-02 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 01:13:20 11.285u 0.427s 0:12.36 94.6% 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 01:13:20 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 = 2623 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 2.666400 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): -34.14900 19.69500 ymin,ymax (A): 15.45300 75.53400 zmin,zma (A): 16.90200 60.10100 x,y,z range (A): 53.84400 60.08100 43.19900 scale (grids/A): 2.666400 object centre (A): -7.227001 45.49350 38.50150 number of atom coordinates read : 2623 total number of charged atoms : 2481 net assigned charge : 3.500015 assigned positive charge : 393.5078 centred at (gu) : 86.51178 91.38987 91.14876 assigned negative charge : -390.0085 centred at (gu) : 86.49451 92.64537 90.37089 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 155247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21741 grid for indexing accessible points = 1.400000 m= 74361 mr = 114468 m= 23394 mr = 60839 m= 4820 mr = 18513 m= 421 mr = 3593 m= 8 mr = 245 m= 0 mr = 2 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 4140 time to turn everything in is 1.360000 number of dielectric boundary points 60591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 19838 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) : 1.777600 object centre at (A) : -7.227001 45.49350 38.50150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5580262E-02 0.2754799 midg,1,midg; midg,igrid,midg -0.5923137 -0.9071326 1,midg,midg; igrid,midg,midg -7.0547475E-03 5.4404121E-02 gauss-seidel spectral radius is 0.9991972 estimated iterations to convergence 279 setup time was (sec) 1.680000 now iterating at: 01:13:22 rms-change max change #iterations 8.867752 309.3327 at 10iterations 5.028316 124.4396 at 20iterations 2.833719 54.73459 at 30iterations 1.597074 35.87909 at 40iterations 0.8957291 17.56633 at 50iterations 0.5047236 11.04599 at 60iterations 0.2835047 5.709713 at 70iterations 0.1589594 3.210999 at 80iterations 8.9304209E-02 1.888863 at 90iterations 5.0093904E-02 0.9772797 at 100iterations 2.8172538E-02 0.5253057 at 110iterations 1.5805626E-02 0.3155045 at 120iterations 8.9279562E-03 0.1682587 at 130iterations 5.0285491E-03 9.9431038E-02 at 140iterations 2.8614230E-03 5.5156708E-02 at 150iterations 1.6474003E-03 3.9737701E-02 at 160iterations 9.7031961E-04 2.0866394E-02 at 170iterations 5.9014949E-04 1.3889313E-02 at 180iterations finished qdiffx linear iterations at : 01:13:38 total time elapsed so far: 18.24000 # loops : 180 mean,max change (kT/e) : 5.9014949E-04 1.3889313E-02 energy calculations done at 18.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.41000 DelPhi exited at 01:13:39 18.419u 0.470s 0:19.39 97.3% 0+0k 0+0io 0pf+0w