Sun Oct 9 07:49:06 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 07:49:06 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6972327 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): -16.39100 31.14000 ymin,ymax (A): -20.27900 30.78000 zmin,zma (A): -4.483000 34.78100 x,y,z range (A): 47.53100 51.05900 39.26400 scale (grids/A): 0.6972327 object centre (A): 7.374499 5.250500 15.14900 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 332.2636 centred at (gu) : 89.85760 90.48463 90.80682 assigned negative charge : -326.2639 centred at (gu) : 89.76496 90.57476 90.93233 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7231 nv = 96 ne = 84 npr = 45795 no. pairs analyzed = 45795 no. exposed pairs = 2787 no. arc points = 19966 no. surface atoms = 944 nbur = 1267 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 483 mr = 3966 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.1800000 number of dielectric boundary points 3683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1884 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8206 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7878617E-08 -1.4259966E-08 midg,1,midg; midg,igrid,midg 7.0070932E-08 3.1775642E-09 1,midg,midg; igrid,midg,midg 2.0564268E-09 7.5896722E-08 gauss-seidel spectral radius is 0.9892985 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 07:49:07 rms-change max change #iterations 0.1937056 29.60646 at 10iterations 2.2767490E-02 3.747390 at 20iterations 2.7133103E-03 0.3493602 at 30iterations 3.2965018E-04 4.4187546E-02 at 40iterations 3.8806244E-05 5.9967041E-03 at 50iterations finished qdiffx linear iterations at : 07:49:10 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.8806244E-05 5.9967041E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 07:49:10 3.384u 0.161s 0:03.83 92.4% 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 07:49:10 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.091698 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): -16.39100 31.14000 ymin,ymax (A): -20.27900 30.78000 zmin,zma (A): -4.483000 34.78100 x,y,z range (A): 47.53100 51.05900 39.26400 scale (grids/A): 2.091698 object centre (A): 7.374499 5.250500 15.14900 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 332.2636 centred at (gu) : 89.57280 91.45342 92.42026 assigned negative charge : -326.2639 centred at (gu) : 89.29490 91.72424 92.79701 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19966 grid for indexing accessible points = 1.400000 m= 30219 mr = 52232 m= 5930 mr = 22841 m= 595 mr = 3933 m= 23 mr = 286 m= 0 mr = 7 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2820 time to turn everything in is 0.3800000 number of dielectric boundary points 33719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16454 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) : 0.6972327 object centre at (A) : 7.374499 5.250500 15.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9104100E-02 9.6447812E-03 midg,1,midg; midg,igrid,midg 3.6098734E-02 2.2124134E-02 1,midg,midg; igrid,midg,midg -7.3059378E-03 3.4122288E-02 gauss-seidel spectral radius is 0.9988199 estimated iterations to convergence 230 setup time was (sec) 0.5900000 now iterating at: 07:49:11 rms-change max change #iterations 4.691561 223.5496 at 10iterations 2.295721 90.43608 at 20iterations 1.134348 40.78556 at 30iterations 0.5622846 18.74126 at 40iterations 0.2775029 8.386368 at 50iterations 0.1365452 4.066814 at 60iterations 6.7659542E-02 2.035070 at 70iterations 3.3377729E-02 0.9651794 at 80iterations 1.6428171E-02 0.5879339 at 90iterations 8.1193410E-03 0.2562866 at 100iterations 4.0209023E-03 0.1365919 at 110iterations 1.9808786E-03 5.7712078E-02 at 120iterations finished qdiffx linear iterations at : 07:49:18 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.9808786E-03 5.7712078E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 07:49:19 7.812u 0.208s 0:08.35 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 Sun Oct 9 2011 at 07:49:19 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.137547 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): -16.39100 31.14000 ymin,ymax (A): -20.27900 30.78000 zmin,zma (A): -4.483000 34.78100 x,y,z range (A): 47.53100 51.05900 39.26400 scale (grids/A): 3.137547 object centre (A): 7.374499 5.250500 15.14900 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 332.2636 centred at (gu) : 89.35912 92.18021 93.63030 assigned negative charge : -326.2639 centred at (gu) : 88.94231 92.58630 94.19553 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19966 grid for indexing accessible points = 1.400000 m= 93114 mr = 125605 m= 38494 mr = 76937 m= 11462 mr = 31799 m= 2333 mr = 8846 m= 323 mr = 1602 m= 23 mr = 230 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 9018 time to turn everything in is 1.160000 number of dielectric boundary points 76071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 16592 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) : 2.091698 object centre at (A) : 7.374499 5.250500 15.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5691282 4.5575362E-02 midg,1,midg; midg,igrid,midg 0.3506767 0.3059948 1,midg,midg; igrid,midg,midg -1.2572723E-02 0.2596096 gauss-seidel spectral radius is 0.9992909 estimated iterations to convergence 296 setup time was (sec) 1.420000 now iterating at: 07:49:20 rms-change max change #iterations 10.36728 387.4034 at 10iterations 6.021828 118.9240 at 20iterations 3.500086 69.24451 at 30iterations 2.030704 37.28874 at 40iterations 1.180899 19.87105 at 50iterations 0.6866291 11.69063 at 60iterations 0.3987720 7.281750 at 70iterations 0.2317503 3.838203 at 80iterations 0.1342817 2.391207 at 90iterations 7.7945083E-02 1.416760 at 100iterations 4.5330465E-02 0.8300991 at 110iterations 2.6277831E-02 0.5002580 at 120iterations 1.5244121E-02 0.2513647 at 130iterations 8.8659478E-03 0.1523199 at 140iterations 5.1305206E-03 8.7925911E-02 at 150iterations 2.9849675E-03 5.1219940E-02 at 160iterations 1.7340675E-03 3.0893326E-02 at 170iterations 1.0043223E-03 1.7784119E-02 at 180iterations finished qdiffx linear iterations at : 07:49:32 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.0043223E-03 1.7784119E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 07:49:32 12.952u 0.183s 0:13.44 97.6% 0+0k 0+0io 0pf+0w