Mon Oct 10 00:05:16 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 00:05:16 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 = 3097 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: 0.6280765 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): -34.87500 19.25300 ymin,ymax (A): -13.16200 37.93600 zmin,zma (A): -14.95400 41.72700 x,y,z range (A): 54.12800 51.09800 56.68100 scale (grids/A): 0.6280765 object centre (A): -7.811000 12.38700 13.38650 number of atom coordinates read : 3097 total number of charged atoms : 2955 net assigned charge : 2.500006 assigned positive charge : 466.1549 centred at (gu) : 90.92432 90.39437 91.64272 assigned negative charge : -463.6563 centred at (gu) : 90.88951 90.29673 91.62225 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8157 nv = 96 ne = 84 npr = 61500 no. pairs analyzed = 61500 no. exposed pairs = 4059 no. arc points = 28819 no. surface atoms = 1353 nbur = 1744 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 4287 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2300000 number of dielectric boundary points 4257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2895 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 10055 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1375330E-10 6.4067018E-09 midg,1,midg; midg,igrid,midg -6.7681216E-09 1.3173667E-08 1,midg,midg; igrid,midg,midg -8.2483087E-10 7.2234947E-09 gauss-seidel spectral radius is 0.9869190 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 00:05:16 rms-change max change #iterations 0.1426992 18.66226 at 10iterations 1.3636418E-02 1.754549 at 20iterations 1.2801728E-03 0.1442890 at 30iterations 1.2756817E-04 1.7459869E-02 at 40iterations 1.3134263E-05 1.7297268E-03 at 50iterations finished qdiffx linear iterations at : 00:05:19 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.3134263E-05 1.7297268E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 00:05:20 3.461u 0.178s 0:03.92 92.6% 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 Mon Oct 10 2011 at 00:05:20 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 = 3097 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: 1.884229 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): -34.87500 19.25300 ymin,ymax (A): -13.16200 37.93600 zmin,zma (A): -14.95400 41.72700 x,y,z range (A): 54.12800 51.09800 56.68100 scale (grids/A): 1.884229 object centre (A): -7.811000 12.38700 13.38650 number of atom coordinates read : 3097 total number of charged atoms : 2955 net assigned charge : 2.500006 assigned positive charge : 466.1549 centred at (gu) : 92.77237 91.18280 94.92734 assigned negative charge : -463.6563 centred at (gu) : 92.66820 90.89028 94.86626 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 88427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28819 grid for indexing accessible points = 1.400000 m= 29399 mr = 59699 m= 4143 mr = 20845 m= 211 mr = 2352 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1522 time to turn everything in is 0.4500000 number of dielectric boundary points 39242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 23183 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) : 0.6280765 object centre at (A) : -7.811000 12.38700 13.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5491369E-02 -1.7910007E-03 midg,1,midg; midg,igrid,midg -1.3452888E-03 1.9470321E-02 1,midg,midg; igrid,midg,midg -1.5884981E-02 6.1918586E-03 gauss-seidel spectral radius is 0.9986659 estimated iterations to convergence 217 setup time was (sec) 0.6600000 now iterating at: 00:05:21 rms-change max change #iterations 4.613532 170.5880 at 10iterations 2.158376 76.40947 at 20iterations 1.018666 31.71624 at 30iterations 0.4814839 14.40807 at 40iterations 0.2272422 6.615074 at 50iterations 0.1073060 3.166180 at 60iterations 5.0508641E-02 1.491699 at 70iterations 2.3883000E-02 0.6870708 at 80iterations 1.1259822E-02 0.3257980 at 90iterations 5.3210389E-03 0.1673584 at 100iterations 2.5162650E-03 7.0333481E-02 at 110iterations 1.1875820E-03 3.6771297E-02 at 120iterations finished qdiffx linear iterations at : 00:05:28 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 1.1875820E-03 3.6771297E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 00:05:28 8.051u 0.206s 0:08.60 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 Mon Oct 10 2011 at 00:05:28 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 = 3097 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: 2.826344 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): -34.87500 19.25300 ymin,ymax (A): -13.16200 37.93600 zmin,zma (A): -14.95400 41.72700 x,y,z range (A): 54.12800 51.09800 56.68100 scale (grids/A): 2.826344 object centre (A): -7.811000 12.38700 13.38650 number of atom coordinates read : 3097 total number of charged atoms : 2955 net assigned charge : 2.500006 assigned positive charge : 466.1549 centred at (gu) : 94.15829 91.77391 97.39104 assigned negative charge : -463.6563 centred at (gu) : 94.00241 91.33519 97.29927 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 204547 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28819 grid for indexing accessible points = 1.400000 m= 97162 mr = 145287 m= 32224 mr = 77833 m= 7193 mr = 25064 m= 915 mr = 5052 m= 44 mr = 543 m= 0 mr = 2 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 5203 time to turn everything in is 1.090000 number of dielectric boundary points 88304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 23633 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) : 1.884229 object centre at (A) : -7.811000 12.38700 13.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1845769 -9.1678888E-02 midg,1,midg; midg,igrid,midg 6.1375991E-02 -4.3953493E-02 1,midg,midg; igrid,midg,midg -0.2745549 -2.8435532E-02 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 1.330000 now iterating at: 00:05:30 rms-change max change #iterations 11.07684 332.1790 at 10iterations 6.646834 168.8345 at 20iterations 3.956464 81.22201 at 30iterations 2.338532 49.43835 at 40iterations 1.378392 25.42001 at 50iterations 0.8095069 15.03440 at 60iterations 0.4741997 8.215755 at 70iterations 0.2780306 4.664894 at 80iterations 0.1621993 2.834229 at 90iterations 9.4717413E-02 1.746258 at 100iterations 5.5125684E-02 0.9192896 at 110iterations 3.2131907E-02 0.5416894 at 120iterations 1.8735547E-02 0.3119869 at 130iterations 1.0910848E-02 0.1777492 at 140iterations 6.3557732E-03 0.1181297 at 150iterations 3.6963427E-03 5.9026718E-02 at 160iterations 2.1501612E-03 3.8472176E-02 at 170iterations 1.2514420E-03 2.2413373E-02 at 180iterations finished qdiffx linear iterations at : 00:05:42 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 1.2514420E-03 2.2413373E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 00:05:42 13.290u 0.228s 0:13.79 97.9% 0+0k 0+0io 0pf+0w