Sat Oct 8 17:53:46 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 17:53:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3763 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5522633 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): -1.822000 60.42800 ymin,ymax (A): -18.50800 44.52500 zmin,zma (A): -5.357000 59.10500 x,y,z range (A): 62.25000 63.03300 64.46201 scale (grids/A): 0.5522633 object centre (A): 29.30300 13.00850 26.87400 number of atom coordinates read : 3763 total number of charged atoms : 3612 net assigned charge : -8.999964 assigned positive charge : 566.9893 centred at (gu) : 88.85362 86.67175 90.52241 assigned negative charge : -575.9918 centred at (gu) : 88.93652 86.67431 90.53395 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7573 nv = 96 ne = 84 npr = 75506 no. pairs analyzed = 75506 no. exposed pairs = 4950 no. arc points = 34803 no. surface atoms = 1638 nbur = 2125 mkacc time = 0.2500000 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 = 1.540000 m= 336 mr = 3907 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.3199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 3990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3507 ## 439 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 9858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2343713E-10 -9.5027075E-10 midg,1,midg; midg,igrid,midg -1.5374609E-09 -3.4127398E-10 1,midg,midg; igrid,midg,midg 2.2845378E-10 -1.2193500E-09 gauss-seidel spectral radius is 0.9831561 estimated iterations to convergence 63 setup time was (sec) 0.8000000 now iterating at: 17:53:47 rms-change max change #iterations 8.6738817E-02 15.23553 at 10iterations 6.2054708E-03 0.8713188 at 20iterations 5.4532191E-04 8.1398010E-02 at 30iterations 1.0149957E-04 1.7821312E-02 at 40iterations 2.8105915E-05 4.8208237E-03 at 50iterations finished qdiffx linear iterations at : 17:53:51 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 2.8105915E-05 4.8208237E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 17:53:51 4.621u 0.443s 0:05.35 94.5% 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 Sat Oct 8 2011 at 17:53:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3763 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.656790 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): -1.822000 60.42800 ymin,ymax (A): -18.50800 44.52500 zmin,zma (A): -5.357000 59.10500 x,y,z range (A): 62.25000 63.03300 64.46201 scale (grids/A): 1.656790 object centre (A): 29.30300 13.00850 26.87400 number of atom coordinates read : 3763 total number of charged atoms : 3612 net assigned charge : -8.999964 assigned positive charge : 566.9893 centred at (gu) : 86.55996 80.01383 91.56615 assigned negative charge : -575.9918 centred at (gu) : 86.80907 80.02230 91.60126 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 83774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34803 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26684 mr = 56854 m= 2875 mr = 18153 m= 80 mr = 1335 m= 0 mr = 5 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.8600000 number of dielectric boundary points 37066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 390 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 27741 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) : 0.5522633 object centre at (A) : 29.30300 13.00850 26.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7869644E-04 -3.3018147E-03 midg,1,midg; midg,igrid,midg -2.8282078E-02 -8.8774944E-03 1,midg,midg; igrid,midg,midg -1.1673596E-02 -3.4946069E-02 gauss-seidel spectral radius is 0.9983146 estimated iterations to convergence 193 setup time was (sec) 1.190000 now iterating at: 17:53:53 rms-change max change #iterations 3.930577 171.6319 at 10iterations 1.686027 59.60041 at 20iterations 0.7276898 25.11199 at 30iterations 0.3131893 10.01117 at 40iterations 0.1349149 4.802984 at 50iterations 5.8058735E-02 1.751734 at 60iterations 2.4939187E-02 0.8234024 at 70iterations 1.0770760E-02 0.3256187 at 80iterations 4.6692207E-03 0.1428833 at 90iterations 2.0307326E-03 6.9336891E-02 at 100iterations 8.9998788E-04 2.9962540E-02 at 110iterations 4.0896374E-04 1.3158381E-02 at 120iterations finished qdiffx linear iterations at : 17:54:02 total time elapsed so far: 10.29000 # loops : 120 mean,max change (kT/e) : 4.0896374E-04 1.3158381E-02 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 17:54:03 10.508u 0.478s 0:11.26 97.4% 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 Sat Oct 8 2011 at 17:54:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3763 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.485185 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): -1.822000 60.42800 ymin,ymax (A): -18.50800 44.52500 zmin,zma (A): -5.357000 59.10500 x,y,z range (A): 62.25000 63.03300 64.46201 scale (grids/A): 2.485185 object centre (A): 29.30300 13.00850 26.87400 number of atom coordinates read : 3763 total number of charged atoms : 3612 net assigned charge : -8.999964 assigned positive charge : 566.9893 centred at (gu) : 84.83961 75.02050 92.34886 assigned negative charge : -575.9918 centred at (gu) : 85.21355 75.03339 92.40188 start vw surface at 0.2000000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 194305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34803 grid for indexing accessible points = 1.400000 m= 91762 mr = 139008 m= 26470 mr = 72183 m= 4404 mr = 19534 m= 339 mr = 2720 m= 6 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 2.160000 number of dielectric boundary points 83715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 28863 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) : 1.656790 object centre at (A) : 29.30300 13.00850 26.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1766597E-02 0.1479492 midg,1,midg; midg,igrid,midg -0.4364766 -0.1077345 1,midg,midg; igrid,midg,midg -0.1847245 -0.6259536 gauss-seidel spectral radius is 0.9991969 estimated iterations to convergence 279 setup time was (sec) 2.530000 now iterating at: 17:54:06 rms-change max change #iterations 10.17941 344.9669 at 10iterations 5.859977 122.6555 at 20iterations 3.354627 73.70372 at 30iterations 1.905711 37.04618 at 40iterations 1.082568 23.06923 at 50iterations 0.6121062 12.33512 at 60iterations 0.3466558 6.690830 at 70iterations 0.1950465 3.808867 at 80iterations 0.1097458 2.052855 at 90iterations 6.1808206E-02 1.120389 at 100iterations 3.4793291E-02 0.6255428 at 110iterations 1.9598255E-02 0.3566387 at 120iterations 1.0995635E-02 0.1972386 at 130iterations 6.1916197E-03 0.1276474 at 140iterations 3.4810239E-03 6.4675331E-02 at 150iterations 1.9565220E-03 3.8735747E-02 at 160iterations 1.1080598E-03 2.0332813E-02 at 170iterations 6.2650244E-04 1.2392998E-02 at 180iterations finished qdiffx linear iterations at : 17:54:21 total time elapsed so far: 18.10000 # loops : 180 mean,max change (kT/e) : 6.2650244E-04 1.2392998E-02 energy calculations done at 18.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.32000 DelPhi exited at 17:54:22 18.326u 0.497s 0:19.09 98.5% 0+0k 0+0io 0pf+0w