Sat Oct 8 13:57:06 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 Sat Oct 8 2011 at 13:57:06 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 = 3027 !!! WARNING: NAP 500 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6524329 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): -11.97300 42.15700 ymin,ymax (A): -23.59900 22.33200 zmin,zma (A): -7.208000 47.35700 x,y,z range (A): 54.13000 45.93100 54.56500 scale (grids/A): 0.6524329 object centre (A): 15.09200 -0.6335001 20.07450 number of atom coordinates read : 3027 total number of charged atoms : 2880 net assigned charge : 7.1674585E-06 assigned positive charge : 453.4955 centred at (gu) : 88.99607 90.05102 91.60954 assigned negative charge : -453.4963 centred at (gu) : 88.97840 89.95470 91.52707 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8532 nv = 96 ne = 84 npr = 63428 no. pairs analyzed = 63428 no. exposed pairs = 3472 no. arc points = 23963 no. surface atoms = 1180 nbur = 1847 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 462 mr = 4970 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3200000 number of dielectric boundary points 3977 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2375 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10300 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1361909E-08 2.1604043E-08 midg,1,midg; midg,igrid,midg -1.8466739E-08 1.8010157E-08 1,midg,midg; igrid,midg,midg -4.4617319E-09 2.5032376E-09 gauss-seidel spectral radius is 0.9878570 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 13:57:06 rms-change max change #iterations 0.1758400 21.54623 at 10iterations 1.8449416E-02 2.173854 at 20iterations 2.0262196E-03 0.2616463 at 30iterations 2.5324652E-04 3.3449173E-02 at 40iterations 4.0922405E-05 5.5160522E-03 at 50iterations finished qdiffx linear iterations at : 13:57:09 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 4.0922405E-05 5.5160522E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 13:57:09 3.165u 0.150s 0:03.61 91.6% 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 Sat Oct 8 2011 at 13:57:09 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 = 3027 !!! WARNING: NAP 500 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.957299 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): -11.97300 42.15700 ymin,ymax (A): -23.59900 22.33200 zmin,zma (A): -7.208000 47.35700 x,y,z range (A): 54.13000 45.93100 54.56500 scale (grids/A): 1.957299 object centre (A): 15.09200 -0.6335001 20.07450 number of atom coordinates read : 3027 total number of charged atoms : 2880 net assigned charge : 7.1674585E-06 assigned positive charge : 453.4955 centred at (gu) : 86.98762 90.15251 94.82825 assigned negative charge : -453.4963 centred at (gu) : 86.93482 89.86389 94.58092 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 92815 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23963 grid for indexing accessible points = 1.400000 m= 34351 mr = 67164 m= 5410 mr = 25887 m= 363 mr = 3403 m= 4 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 36380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22766 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) : 0.6524329 object centre at (A) : 15.09200 -0.6335001 20.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1624159E-02 2.7524322E-02 midg,1,midg; midg,igrid,midg -1.5644331E-03 2.4826657E-02 1,midg,midg; igrid,midg,midg -4.4334352E-02 1.8022431E-02 gauss-seidel spectral radius is 0.9987375 estimated iterations to convergence 223 setup time was (sec) 0.8900000 now iterating at: 13:57:10 rms-change max change #iterations 4.872142 181.9152 at 10iterations 2.362106 74.22891 at 20iterations 1.134067 34.84359 at 30iterations 0.5510179 14.57443 at 40iterations 0.2654580 6.997828 at 50iterations 0.1283052 3.706752 at 60iterations 6.1924674E-02 1.603815 at 70iterations 2.9887782E-02 0.8461246 at 80iterations 1.4475752E-02 0.3824387 at 90iterations 6.9880057E-03 0.1960564 at 100iterations 3.3851557E-03 9.2942238E-02 at 110iterations 1.6418517E-03 4.9191475E-02 at 120iterations finished qdiffx linear iterations at : 13:57:17 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 1.6418517E-03 4.9191475E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 13:57:17 7.419u 0.182s 0:07.89 96.1% 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 Sat Oct 8 2011 at 13:57:17 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 = 3027 !!! WARNING: NAP 500 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.935948 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): -11.97300 42.15700 ymin,ymax (A): -23.59900 22.33200 zmin,zma (A): -7.208000 47.35700 x,y,z range (A): 54.13000 45.93100 54.56500 scale (grids/A): 2.935948 object centre (A): 15.09200 -0.6335001 20.07450 number of atom coordinates read : 3027 total number of charged atoms : 2880 net assigned charge : 7.1674585E-06 assigned positive charge : 453.4955 centred at (gu) : 85.48134 90.22869 97.24221 assigned negative charge : -453.4963 centred at (gu) : 85.40208 89.79579 96.87127 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 215087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23963 grid for indexing accessible points = 1.400000 m= 111734 mr = 162157 m= 40479 mr = 93302 m= 9810 mr = 32899 m= 1535 mr = 7248 m= 93 mr = 1022 m= 6 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 82091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 23039 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) : 1.957299 object centre at (A) : 15.09200 -0.6335001 20.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1333009E-02 0.5145365 midg,1,midg; midg,igrid,midg -8.4171779E-03 0.2784223 1,midg,midg; igrid,midg,midg -0.4595026 0.2628790 gauss-seidel spectral radius is 0.9992894 estimated iterations to convergence 296 setup time was (sec) 1.890000 now iterating at: 13:57:19 rms-change max change #iterations 11.22260 366.7794 at 10iterations 6.606050 127.5816 at 20iterations 3.874590 69.23107 at 30iterations 2.268140 43.73835 at 40iterations 1.326421 21.33395 at 50iterations 0.7742722 13.32528 at 60iterations 0.4516564 7.835197 at 70iterations 0.2629915 4.456424 at 80iterations 0.1531851 2.466511 at 90iterations 8.9241415E-02 1.307366 at 100iterations 5.1948976E-02 0.7974281 at 110iterations 3.0218424E-02 0.5163269 at 120iterations 1.7613849E-02 0.3011322 at 130iterations 1.0288075E-02 0.1617074 at 140iterations 6.0102837E-03 9.7785383E-02 at 150iterations 3.5096833E-03 5.9576035E-02 at 160iterations 2.0671501E-03 3.3617020E-02 at 170iterations 1.2258398E-03 2.0336151E-02 at 180iterations finished qdiffx linear iterations at : 13:57:29 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 1.2258398E-03 2.0336151E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 13:57:29 11.723u 0.174s 0:12.20 97.4% 0+0k 0+0io 0pf+0w