Sun Oct 9 02:09:08 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+sph2.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 = amb2.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 02:09:08 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6693617 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): 40.36900 93.55400 ymin,ymax (A): 49.32400 101.8710 zmin,zma (A): -106.6660 -63.45800 x,y,z range (A): 53.18500 52.54700 43.20800 scale (grids/A): 0.6693617 object centre (A): 66.96150 75.59750 -85.06200 number of atom coordinates read : 2382 total number of charged atoms : 2246 net assigned charge : 11.01402 assigned positive charge : 352.5443 centred at (gu) : 89.58472 87.97671 89.63095 assigned negative charge : -341.5310 centred at (gu) : 89.62106 88.05550 89.72595 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7252 nv = 96 ne = 84 npr = 48119 no. pairs analyzed = 48119 no. exposed pairs = 3187 no. arc points = 22376 no. surface atoms = 1069 nbur = 1313 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 456 mr = 3780 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2139 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8400 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0293750E-08 1.3295985E-08 midg,1,midg; midg,igrid,midg 7.9285357E-08 1.2287416E-08 1,midg,midg; igrid,midg,midg 4.6990248E-08 2.5166457E-08 gauss-seidel spectral radius is 0.9884164 estimated iterations to convergence 76 setup time was (sec) 0.5200000 now iterating at: 02:09:09 rms-change max change #iterations 0.1657660 24.93213 at 10iterations 1.8230092E-02 2.512932 at 20iterations 2.1556537E-03 0.2952404 at 30iterations 3.6218812E-04 4.8805237E-02 at 40iterations 9.7270276E-05 1.4017105E-02 at 50iterations finished qdiffx linear iterations at : 02:09:11 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 9.7270276E-05 1.4017105E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 02:09:12 3.316u 0.190s 0:03.77 92.8% 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 02:09:12 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.008085 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): 40.36900 93.55400 ymin,ymax (A): 49.32400 101.8710 zmin,zma (A): -106.6660 -63.45800 x,y,z range (A): 53.18500 52.54700 43.20800 scale (grids/A): 2.008085 object centre (A): 66.96150 75.59750 -85.06200 number of atom coordinates read : 2382 total number of charged atoms : 2246 net assigned charge : 11.01402 assigned positive charge : 352.5443 centred at (gu) : 88.75375 83.92962 88.89249 assigned negative charge : -341.5310 centred at (gu) : 88.86310 84.16660 89.17800 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77042 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22376 grid for indexing accessible points = 1.400000 m= 28563 mr = 51746 m= 5362 mr = 20409 m= 399 mr = 3260 m= 6 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 555 time to turn everything in is 0.5700000 number of dielectric boundary points 35821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17778 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) : 0.6693617 object centre at (A) : 66.96150 75.59750 -85.06200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9633345E-02 4.2771418E-03 midg,1,midg; midg,igrid,midg 5.8102399E-02 3.0419633E-02 1,midg,midg; igrid,midg,midg 7.0242912E-02 1.6587695E-02 gauss-seidel spectral radius is 0.9987530 estimated iterations to convergence 224 setup time was (sec) 0.8400000 now iterating at: 02:09:13 rms-change max change #iterations 4.440356 186.6020 at 10iterations 2.146383 73.75885 at 20iterations 1.034886 33.57243 at 30iterations 0.4990444 15.32885 at 40iterations 0.2408733 8.663101 at 50iterations 0.1167051 3.509674 at 60iterations 5.6456964E-02 1.809437 at 70iterations 2.7470488E-02 0.8592110 at 80iterations 1.3296655E-02 0.4349995 at 90iterations 6.4873933E-03 0.2080460 at 100iterations 3.1960080E-03 9.9922180E-02 at 110iterations 1.6039767E-03 5.0498962E-02 at 120iterations finished qdiffx linear iterations at : 02:09:19 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 1.6039767E-03 5.0498962E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 02:09:20 7.496u 0.247s 0:08.02 96.3% 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 02:09:20 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 3.012128 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): 40.36900 93.55400 ymin,ymax (A): 49.32400 101.8710 zmin,zma (A): -106.6660 -63.45800 x,y,z range (A): 53.18500 52.54700 43.20800 scale (grids/A): 3.012128 object centre (A): 66.96150 75.59750 -85.06200 number of atom coordinates read : 2382 total number of charged atoms : 2246 net assigned charge : 11.01402 assigned positive charge : 352.5443 centred at (gu) : 88.13056 80.89433 88.33867 assigned negative charge : -341.5310 centred at (gu) : 88.29472 81.24988 88.76702 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 177667 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22376 grid for indexing accessible points = 1.400000 m= 89998 mr = 125758 m= 35160 mr = 71944 m= 9832 mr = 27585 m= 1712 mr = 7204 m= 139 mr = 1107 m= 4 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 1924 time to turn everything in is 1.460000 number of dielectric boundary points 80850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 17968 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) : 2.008085 object centre at (A) : 66.96150 75.59750 -85.06200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2408577 2.3771722E-03 midg,1,midg; midg,igrid,midg 0.5079622 0.3846009 1,midg,midg; igrid,midg,midg 0.6345493 -1.9741924E-02 gauss-seidel spectral radius is 0.9992973 estimated iterations to convergence 298 setup time was (sec) 1.790000 now iterating at: 02:09:22 rms-change max change #iterations 10.32919 379.7711 at 10iterations 6.157158 150.2156 at 20iterations 3.661249 82.85851 at 30iterations 2.164496 44.01608 at 40iterations 1.276527 28.28317 at 50iterations 0.7498050 15.55578 at 60iterations 0.4397992 9.069160 at 70iterations 0.2576766 5.283829 at 80iterations 0.1512944 2.691892 at 90iterations 8.8578813E-02 1.603043 at 100iterations 5.1773690E-02 0.9428024 at 110iterations 3.0255735E-02 0.6355286 at 120iterations 1.7765377E-02 0.3592911 at 130iterations 1.0422674E-02 0.2083111 at 140iterations 6.1216489E-03 0.1120377 at 150iterations 3.6307208E-03 6.8975925E-02 at 160iterations 2.1789013E-03 4.1038513E-02 at 170iterations 1.3399930E-03 2.6359558E-02 at 180iterations finished qdiffx linear iterations at : 02:09:32 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.3399930E-03 2.6359558E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 02:09:33 12.586u 0.223s 0:13.08 97.8% 0+0k 0+0io 0pf+0w