Tue Oct 11 05:47:54 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 05:47:54 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN8 812 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: 0.7322090 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): 25.50800 72.09299 ymin,ymax (A): -18.79700 29.82300 zmin,zma (A): 3.738000 46.11800 x,y,z range (A): 46.58500 48.62000 42.38000 scale (grids/A): 0.7322090 object centre (A): 48.80050 5.513000 24.92800 number of atom coordinates read : 2290 total number of charged atoms : 1970 net assigned charge : 7.600008 assigned positive charge : 320.5439 centred at (gu) : 89.17999 90.64780 90.37373 assigned negative charge : -312.9442 centred at (gu) : 89.31788 90.60798 90.44156 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7723 nv = 96 ne = 84 npr = 42026 no. pairs analyzed = 42026 no. exposed pairs = 2543 no. arc points = 17279 no. surface atoms = 864 nbur = 1426 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 559 mr = 4539 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1528 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5756565E-07 5.7708451E-08 midg,1,midg; midg,igrid,midg 6.9681846E-08 1.6399110E-07 1,midg,midg; igrid,midg,midg 2.6493547E-07 -4.3908219E-09 gauss-seidel spectral radius is 0.9902729 estimated iterations to convergence 82 setup time was (sec) 0.5100000 now iterating at: 05:47:55 rms-change max change #iterations 0.2304121 28.35937 at 10iterations 3.0577488E-02 4.461426 at 20iterations 4.1785035E-03 0.5149899 at 30iterations 6.1507331E-04 8.1932068E-02 at 40iterations 1.2521895E-04 1.4301300E-02 at 50iterations finished qdiffx linear iterations at : 05:47:57 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 1.2521895E-04 1.4301300E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 05:47:58 3.304u 0.137s 0:04.01 85.5% 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 05:47:58 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN8 812 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: 2.196627 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): 25.50800 72.09299 ymin,ymax (A): -18.79700 29.82300 zmin,zma (A): 3.738000 46.11800 x,y,z range (A): 46.58500 48.62000 42.38000 scale (grids/A): 2.196627 object centre (A): 48.80050 5.513000 24.92800 number of atom coordinates read : 2290 total number of charged atoms : 1970 net assigned charge : 7.600008 assigned positive charge : 320.5439 centred at (gu) : 87.54024 91.94337 91.12095 assigned negative charge : -312.9442 centred at (gu) : 87.95373 91.82391 91.32472 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 80900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17279 grid for indexing accessible points = 1.400000 m= 33922 mr = 58052 m= 7213 mr = 26135 m= 779 mr = 4962 m= 28 mr = 442 m= 0 mr = 6 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 33245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15672 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) : 0.7322090 object centre at (A) : 48.80050 5.513000 24.92800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8684648E-02 4.0400885E-02 midg,1,midg; midg,igrid,midg 5.5511318E-02 3.7546657E-02 1,midg,midg; igrid,midg,midg 5.8893770E-02 -5.1233642E-02 gauss-seidel spectral radius is 0.9988988 estimated iterations to convergence 238 setup time was (sec) 0.9900000 now iterating at: 05:47:59 rms-change max change #iterations 4.924428 231.3034 at 10iterations 2.483584 78.69118 at 20iterations 1.261355 38.09763 at 30iterations 0.6390787 18.86259 at 40iterations 0.3232122 9.354235 at 50iterations 0.1642971 4.652181 at 60iterations 8.3242930E-02 2.342268 at 70iterations 4.2216532E-02 1.118259 at 80iterations 2.1445733E-02 0.6646147 at 90iterations 1.0923229E-02 0.3078423 at 100iterations 5.5665029E-03 0.1786652 at 110iterations 2.8556203E-03 8.1623077E-02 at 120iterations finished qdiffx linear iterations at : 05:48:06 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 2.8556203E-03 8.1623077E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.330000 DelPhi exited at 05:48:07 8.329u 0.241s 0:09.19 93.1% 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 Tue Oct 11 2011 at 05:48:07 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN8 812 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: 3.294940 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): 25.50800 72.09299 ymin,ymax (A): -18.79700 29.82300 zmin,zma (A): 3.738000 46.11800 x,y,z range (A): 46.58500 48.62000 42.38000 scale (grids/A): 3.294940 object centre (A): 48.80050 5.513000 24.92800 number of atom coordinates read : 2290 total number of charged atoms : 1970 net assigned charge : 7.600008 assigned positive charge : 320.5439 centred at (gu) : 86.31026 92.91499 91.68149 assigned negative charge : -312.9442 centred at (gu) : 86.93065 92.73600 91.98710 start vw surface at 0.1500000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 186264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17279 grid for indexing accessible points = 1.400000 m= 103712 mr = 139145 m= 44709 mr = 87146 m= 13973 mr = 37233 m= 3096 mr = 11060 m= 453 mr = 2382 m= 25 mr = 311 m= 0 mr = 7 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 74948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 15760 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) : 2.196627 object centre at (A) : 48.80050 5.513000 24.92800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1448418 0.3336441 midg,1,midg; midg,igrid,midg 0.4232632 0.1942956 1,midg,midg; igrid,midg,midg 0.5409696 -0.6161300 gauss-seidel spectral radius is 0.9993144 estimated iterations to convergence 301 setup time was (sec) 2.450000 now iterating at: 05:48:10 rms-change max change #iterations 10.77514 292.9114 at 10iterations 6.413908 138.4781 at 20iterations 3.811790 98.24396 at 30iterations 2.268991 39.45572 at 40iterations 1.340917 24.66111 at 50iterations 0.7941512 14.28090 at 60iterations 0.4693174 8.188507 at 70iterations 0.2767166 4.855880 at 80iterations 0.1632363 2.851553 at 90iterations 9.6578963E-02 2.043369 at 100iterations 5.7079028E-02 1.105215 at 110iterations 3.3796094E-02 0.5774765 at 120iterations 2.0097243E-02 0.3450298 at 130iterations 1.2045531E-02 0.2030411 at 140iterations 7.3506702E-03 0.1244774 at 150iterations 4.5875050E-03 8.9725494E-02 at 160iterations 2.9845869E-03 6.0787201E-02 at 170iterations 2.0590958E-03 4.1465759E-02 at 180iterations finished qdiffx linear iterations at : 05:48:22 total time elapsed so far: 14.10000 # loops : 180 mean,max change (kT/e) : 2.0590958E-03 4.1465759E-02 energy calculations done at 14.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.28000 DelPhi exited at 05:48:22 14.286u 0.268s 0:15.04 96.6% 0+0k 0+0io 0pf+0w