Mon Oct 10 10:41:35 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 10:41:35 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5296 !!! WARNING: ADP 1585 has a net charge of -2.0000 !!! WARNING: ADP 1587 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5233370 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): -26.93900 40.13000 ymin,ymax (A): -43.85600 24.16900 zmin,zma (A): -36.31500 26.99500 x,y,z range (A): 67.06900 68.02500 63.31000 scale (grids/A): 0.5233370 object centre (A): 6.595501 -9.843499 -4.660000 number of atom coordinates read : 5296 total number of charged atoms : 5140 net assigned charge : 6.500019 assigned positive charge : 841.5606 centred at (gu) : 89.28502 90.95800 90.42056 assigned negative charge : -835.0687 centred at (gu) : 89.28271 90.90237 90.39542 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 9344 nv = 96 ne = 84 npr = 105231 no. pairs analyzed = 105231 no. exposed pairs = 6358 no. arc points = 42250 no. surface atoms = 2140 nbur = 3156 mkacc time = 0.3000000 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 = 1.624000 m= 352 mr = 5225 m= 0 mr = 9 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 4462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4287 ## 581 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 12417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4723066E-11 3.1836020E-10 midg,1,midg; midg,igrid,midg -1.0150836E-10 5.6571664E-10 1,midg,midg; igrid,midg,midg 1.7321844E-10 1.4108056E-10 gauss-seidel spectral radius is 0.9813562 estimated iterations to convergence 60 setup time was (sec) 0.8800000 now iterating at: 10:41:37 rms-change max change #iterations 8.2596391E-02 13.98046 at 10iterations 5.2221701E-03 0.7472134 at 20iterations 5.7108537E-04 9.5255852E-02 at 30iterations 1.7256368E-04 3.0240059E-02 at 40iterations 6.6061417E-05 9.6979141E-03 at 50iterations finished qdiffx linear iterations at : 10:41:40 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 6.6061417E-05 9.6979141E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 10:41:40 4.352u 0.252s 0:04.96 92.7% 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 10:41:40 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5296 !!! WARNING: ADP 1585 has a net charge of -2.0000 !!! WARNING: ADP 1587 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.570011 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): -26.93900 40.13000 ymin,ymax (A): -43.85600 24.16900 zmin,zma (A): -36.31500 26.99500 x,y,z range (A): 67.06900 68.02500 63.31000 scale (grids/A): 1.570011 object centre (A): 6.595501 -9.843499 -4.660000 number of atom coordinates read : 5296 total number of charged atoms : 5140 net assigned charge : 6.500019 assigned positive charge : 841.5606 centred at (gu) : 87.85323 92.87228 91.26007 assigned negative charge : -835.0687 centred at (gu) : 87.84819 92.70685 91.18647 start vw surface at 0.2200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 106448 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42250 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 33711 mr = 76634 m= 3108 mr = 23873 m= 65 mr = 1419 m= 0 mr = 4 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 549 time to turn everything in is 0.9100000 number of dielectric boundary points 41402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 592 ## 12 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 38865 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) : 0.5233370 object centre at (A) : 6.595501 -9.843499 -4.660000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8670314E-03 -3.3994429E-04 midg,1,midg; midg,igrid,midg -3.3780549E-02 1.5750894E-02 1,midg,midg; igrid,midg,midg -9.4355410E-03 1.9899150E-02 gauss-seidel spectral radius is 0.9982518 estimated iterations to convergence 190 setup time was (sec) 1.210000 now iterating at: 10:41:42 rms-change max change #iterations 4.389631 164.7479 at 10iterations 1.864266 53.77752 at 20iterations 0.7931355 24.05638 at 30iterations 0.3368252 9.602821 at 40iterations 0.1430927 4.359352 at 50iterations 6.0822822E-02 1.956364 at 60iterations 2.5984500E-02 0.8537521 at 70iterations 1.1085843E-02 0.3364582 at 80iterations 4.7426666E-03 0.1382370 at 90iterations 2.0547896E-03 6.2789917E-02 at 100iterations 9.1443484E-04 2.7364731E-02 at 110iterations 4.3408872E-04 1.4504433E-02 at 120iterations finished qdiffx linear iterations at : 10:41:50 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 4.3408872E-04 1.4504433E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 10:41:51 9.842u 0.315s 0:10.49 96.7% 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 10:41:51 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5296 !!! WARNING: ADP 1585 has a net charge of -2.0000 !!! WARNING: ADP 1587 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.355016 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): -26.93900 40.13000 ymin,ymax (A): -43.85600 24.16900 zmin,zma (A): -36.31500 26.99500 x,y,z range (A): 67.06900 68.02500 63.31000 scale (grids/A): 2.355016 object centre (A): 6.595501 -9.843499 -4.660000 number of atom coordinates read : 5296 total number of charged atoms : 5140 net assigned charge : 6.500019 assigned positive charge : 841.5606 centred at (gu) : 86.77955 94.30802 91.88956 assigned negative charge : -835.0687 centred at (gu) : 86.77225 94.06022 91.77969 start vw surface at 0.2300000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 247494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42250 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 119397 mr = 186597 m= 32383 mr = 96766 m= 4621 mr = 24401 m= 242 mr = 2982 m= 2 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 1.450000 no. cavity mid-points inaccessible to solvent = 1799 time to turn everything in is 2.310000 number of dielectric boundary points 93311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 2.480000 number of grid points assigned charge 41033 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) : 1.570011 object centre at (A) : 6.595501 -9.843499 -4.660000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3871489E-02 -6.5951832E-02 midg,1,midg; midg,igrid,midg -0.7460061 0.2151198 1,midg,midg; igrid,midg,midg -0.3062894 0.4255565 gauss-seidel spectral radius is 0.9992055 estimated iterations to convergence 280 setup time was (sec) 2.650000 now iterating at: 10:41:54 rms-change max change #iterations 11.65115 315.8781 at 10iterations 6.786313 152.4263 at 20iterations 3.918716 85.92199 at 30iterations 2.250951 43.31824 at 40iterations 1.286600 23.12586 at 50iterations 0.7356817 13.60880 at 60iterations 0.4180327 7.941579 at 70iterations 0.2372637 4.105944 at 80iterations 0.1343758 2.519359 at 90iterations 7.6303095E-02 1.265695 at 100iterations 4.3119919E-02 0.7264328 at 110iterations 2.4418198E-02 0.4036107 at 120iterations 1.3807677E-02 0.2573714 at 130iterations 7.8318669E-03 0.1268997 at 140iterations 4.4374680E-03 7.0126534E-02 at 150iterations 2.5243629E-03 4.1980743E-02 at 160iterations 1.4451966E-03 2.4827957E-02 at 170iterations 8.3885092E-04 1.4978886E-02 at 180iterations finished qdiffx linear iterations at : 10:42:08 total time elapsed so far: 16.87000 # loops : 180 mean,max change (kT/e) : 8.3885092E-04 1.4978886E-02 energy calculations done at 16.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.06000 DelPhi exited at 10:42:09 17.057u 0.314s 0:17.65 98.3% 0+0k 0+0io 0pf+0w