Mon Oct 10 16:06:55 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 16:06:56 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 891 has a net charge of 1.4000 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: 0.5903031 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): -31.14600 17.62600 ymin,ymax (A): -8.389999 51.91800 zmin,zma (A): -17.90700 37.85800 x,y,z range (A): 48.77200 60.30800 55.76500 scale (grids/A): 0.5903031 object centre (A): -6.760000 21.76400 9.975499 number of atom coordinates read : 2756 total number of charged atoms : 2611 net assigned charge : 1.700018 assigned positive charge : 405.1806 centred at (gu) : 89.91859 87.46580 87.96748 assigned negative charge : -403.4817 centred at (gu) : 89.96119 87.44463 88.01498 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6466 nv = 96 ne = 84 npr = 55244 no. pairs analyzed = 55244 no. exposed pairs = 3721 no. arc points = 25752 no. surface atoms = 1251 nbur = 1505 mkacc time = 0.1600000 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= 310 mr = 3342 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2473 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7990 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9149239E-09 -4.9811721E-10 midg,1,midg; midg,igrid,midg -1.7147536E-10 6.1594196E-10 1,midg,midg; igrid,midg,midg 1.7094113E-09 -6.6049749E-10 gauss-seidel spectral radius is 0.9851682 estimated iterations to convergence 67 setup time was (sec) 0.6300000 now iterating at: 16:06:56 rms-change max change #iterations 0.1029935 19.22804 at 10iterations 8.4303617E-03 1.495780 at 20iterations 8.7318907E-04 0.1427612 at 30iterations 2.2282828E-04 2.4536133E-02 at 40iterations 8.3664716E-05 9.1724396E-03 at 50iterations finished qdiffx linear iterations at : 16:07:00 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 8.3664716E-05 9.1724396E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 16:07:00 4.091u 0.258s 0:04.62 93.9% 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 16:07:00 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 891 has a net charge of 1.4000 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: 1.770909 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): -31.14600 17.62600 ymin,ymax (A): -8.389999 51.91800 zmin,zma (A): -17.90700 37.85800 x,y,z range (A): 48.77200 60.30800 55.76500 scale (grids/A): 1.770909 object centre (A): -6.760000 21.76400 9.975499 number of atom coordinates read : 2756 total number of charged atoms : 2611 net assigned charge : 1.700018 assigned positive charge : 405.1806 centred at (gu) : 89.75497 82.39668 83.90205 assigned negative charge : -403.4817 centred at (gu) : 89.88344 82.33366 84.04472 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25752 grid for indexing accessible points = 1.400000 m= 23124 mr = 47549 m= 2972 mr = 15927 m= 130 mr = 1570 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 655 time to turn everything in is 0.6300000 number of dielectric boundary points 31550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20301 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) : 0.5903031 object centre at (A) : -6.760000 21.76400 9.975499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1696754E-02 -2.3156484E-03 midg,1,midg; midg,igrid,midg 1.8418656E-03 -2.6647117E-02 1,midg,midg; igrid,midg,midg 5.6956247E-03 -4.7820315E-04 gauss-seidel spectral radius is 0.9984352 estimated iterations to convergence 201 setup time was (sec) 0.9300000 now iterating at: 16:07:01 rms-change max change #iterations 3.768483 155.8334 at 10iterations 1.662399 59.71827 at 20iterations 0.7410307 26.30020 at 30iterations 0.3284192 11.63542 at 40iterations 0.1447514 4.801199 at 50iterations 6.4473815E-02 2.050931 at 60iterations 2.8532950E-02 0.9301624 at 70iterations 1.2714833E-02 0.4259262 at 80iterations 5.7076504E-03 0.1971159 at 90iterations 2.5728259E-03 9.0251446E-02 at 100iterations 1.1929583E-03 4.0316582E-02 at 110iterations 5.8514648E-04 1.9392014E-02 at 120iterations finished qdiffx linear iterations at : 16:07:10 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 5.8514648E-04 1.9392014E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 16:07:10 9.356u 0.303s 0:09.93 97.1% 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 Mon Oct 10 2011 at 16:07:10 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 891 has a net charge of 1.4000 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: 2.656364 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): -31.14600 17.62600 ymin,ymax (A): -8.389999 51.91800 zmin,zma (A): -17.90700 37.85800 x,y,z range (A): 48.77200 60.30800 55.76500 scale (grids/A): 2.656364 object centre (A): -6.760000 21.76400 9.975499 number of atom coordinates read : 2756 total number of charged atoms : 2611 net assigned charge : 1.700018 assigned positive charge : 405.1806 centred at (gu) : 89.63235 78.59484 80.85279 assigned negative charge : -403.4817 centred at (gu) : 89.82495 78.50048 81.06703 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 163245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25752 grid for indexing accessible points = 1.400000 m= 77055 mr = 116591 m= 24677 mr = 60325 m= 4902 mr = 18760 m= 516 mr = 3403 m= 20 mr = 295 m= 0 mr = 4 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 2238 time to turn everything in is 1.580000 number of dielectric boundary points 71037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 20887 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) : 1.770909 object centre at (A) : -6.760000 21.76400 9.975499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1727767 -4.1184681E-03 midg,1,midg; midg,igrid,midg 0.1134356 -0.3931271 1,midg,midg; igrid,midg,midg 3.0680923E-02 -1.1394684E-02 gauss-seidel spectral radius is 0.9992154 estimated iterations to convergence 282 setup time was (sec) 1.900000 now iterating at: 16:07:12 rms-change max change #iterations 9.416927 336.9639 at 10iterations 5.515715 130.2415 at 20iterations 3.203235 82.33258 at 30iterations 1.848883 37.76533 at 40iterations 1.064098 23.16754 at 50iterations 0.6102765 12.45530 at 60iterations 0.3484859 6.942459 at 70iterations 0.1992400 4.516283 at 80iterations 0.1137014 2.474960 at 90iterations 6.4682648E-02 1.319961 at 100iterations 3.6903039E-02 0.7888479 at 110iterations 2.1006182E-02 0.4064412 at 120iterations 1.1906292E-02 0.2304115 at 130iterations 6.7921863E-03 0.1352081 at 140iterations 3.8687200E-03 7.7808917E-02 at 150iterations 2.2174530E-03 5.1861286E-02 at 160iterations 1.2834424E-03 2.7355671E-02 at 170iterations 7.5881358E-04 1.5540600E-02 at 180iterations finished qdiffx linear iterations at : 16:07:26 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 7.5881358E-04 1.5540600E-02 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.64000 DelPhi exited at 16:07:26 15.641u 0.301s 0:16.20 98.3% 0+0k 0+0io 0pf+0w