Sun Oct 9 22:34:41 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 22:34:41 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: SEP 654 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6317321 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): -2.710000 46.04500 ymin,ymax (A): -44.32200 8.059000 zmin,zma (A): -46.67100 9.681999 x,y,z range (A): 48.75500 52.38100 56.35300 scale (grids/A): 0.6317321 object centre (A): 21.66750 -18.13150 -18.49450 number of atom coordinates read : 2565 total number of charged atoms : 2427 net assigned charge : 4.525008 assigned positive charge : 389.4680 centred at (gu) : 91.14007 89.88252 89.47121 assigned negative charge : -384.9436 centred at (gu) : 91.08611 89.88719 89.42484 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6683 nv = 96 ne = 84 npr = 51893 no. pairs analyzed = 51893 no. exposed pairs = 3104 no. arc points = 22448 no. surface atoms = 1059 nbur = 1506 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3546 m= 0 mr = 32 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 76 time to turn everything in is 0.2100000 number of dielectric boundary points 3424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2302 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8251 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1603436E-10 8.3785130E-09 midg,1,midg; midg,igrid,midg 5.7038378E-09 4.5926303E-09 1,midg,midg; igrid,midg,midg 1.6536168E-10 1.2885725E-08 gauss-seidel spectral radius is 0.9870167 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 22:34:42 rms-change max change #iterations 0.1362120 20.74790 at 10iterations 1.3043894E-02 1.897058 at 20iterations 1.2481672E-03 0.1910172 at 30iterations 1.1881493E-04 1.6757965E-02 at 40iterations 1.1416492E-05 1.5296936E-03 at 50iterations finished qdiffx linear iterations at : 22:34:45 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.1416492E-05 1.5296936E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 22:34:45 3.428u 0.163s 0:03.86 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 Sun Oct 9 2011 at 22:34:45 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: SEP 654 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.895196 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): -2.710000 46.04500 ymin,ymax (A): -44.32200 8.059000 zmin,zma (A): -46.67100 9.681999 x,y,z range (A): 48.75500 52.38100 56.35300 scale (grids/A): 1.895196 object centre (A): 21.66750 -18.13150 -18.49450 number of atom coordinates read : 2565 total number of charged atoms : 2427 net assigned charge : 4.525008 assigned positive charge : 389.4680 centred at (gu) : 93.41980 89.64689 88.41341 assigned negative charge : -384.9436 centred at (gu) : 93.25820 89.66158 88.27419 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22448 grid for indexing accessible points = 1.400000 m= 24179 mr = 49710 m= 3559 mr = 17401 m= 205 mr = 2141 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3281 time to turn everything in is 0.3600000 number of dielectric boundary points 31357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19052 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) : 0.6317321 object centre at (A) : 21.66750 -18.13150 -18.49450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3402938E-02 1.4089237E-02 midg,1,midg; midg,igrid,midg -9.6908659E-03 -7.1828789E-04 1,midg,midg; igrid,midg,midg -8.7164659E-03 1.4191389E-02 gauss-seidel spectral radius is 0.9986144 estimated iterations to convergence 213 setup time was (sec) 0.5800000 now iterating at: 22:34:46 rms-change max change #iterations 4.141407 204.4073 at 10iterations 1.920249 69.81441 at 20iterations 0.8925946 27.85690 at 30iterations 0.4167612 13.26029 at 40iterations 0.1930757 7.236416 at 50iterations 9.0001270E-02 2.942763 at 60iterations 4.1922346E-02 1.541645 at 70iterations 1.9515794E-02 0.6309738 at 80iterations 9.0739783E-03 0.2981520 at 90iterations 4.2246343E-03 0.1486816 at 100iterations 1.9641756E-03 6.7855597E-02 at 110iterations 9.1474346E-04 2.9583931E-02 at 120iterations finished qdiffx linear iterations at : 22:34:53 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 9.1474346E-04 2.9583931E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 22:34:54 7.853u 0.200s 0:08.40 95.8% 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 22:34:54 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: SEP 654 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.842794 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): -2.710000 46.04500 ymin,ymax (A): -44.32200 8.059000 zmin,zma (A): -46.67100 9.681999 x,y,z range (A): 48.75500 52.38100 56.35300 scale (grids/A): 2.842794 object centre (A): 21.66750 -18.13150 -18.49450 number of atom coordinates read : 2565 total number of charged atoms : 2427 net assigned charge : 4.525008 assigned positive charge : 389.4680 centred at (gu) : 95.12936 89.47023 87.62000 assigned negative charge : -384.9436 centred at (gu) : 94.88728 89.49240 87.41119 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 168330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22448 grid for indexing accessible points = 1.400000 m= 80470 mr = 120866 m= 26871 mr = 65050 m= 6454 mr = 21101 m= 947 mr = 4767 m= 54 mr = 628 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 10947 time to turn everything in is 0.9100000 number of dielectric boundary points 70689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19413 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) : 1.895196 object centre at (A) : 21.66750 -18.13150 -18.49450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2850441 0.2103298 midg,1,midg; midg,igrid,midg -0.2398819 7.9448521E-02 1,midg,midg; igrid,midg,midg -0.1712074 0.2093304 gauss-seidel spectral radius is 0.9992528 estimated iterations to convergence 289 setup time was (sec) 1.160000 now iterating at: 22:34:55 rms-change max change #iterations 9.710543 407.7549 at 10iterations 5.621927 149.2191 at 20iterations 3.245393 76.69090 at 30iterations 1.868588 37.14361 at 40iterations 1.071466 20.48110 at 50iterations 0.6145403 11.02723 at 60iterations 0.3522423 6.642458 at 70iterations 0.2017478 4.057262 at 80iterations 0.1155048 2.137755 at 90iterations 6.5999947E-02 1.155279 at 100iterations 3.7773993E-02 0.6703758 at 110iterations 2.1613836E-02 0.4075017 at 120iterations 1.2374276E-02 0.2346735 at 130iterations 7.0886770E-03 0.1343002 at 140iterations 4.0524462E-03 7.9128265E-02 at 150iterations 2.3215071E-03 5.0998688E-02 at 160iterations 1.3258966E-03 2.4021149E-02 at 170iterations 7.6004426E-04 1.3595581E-02 at 180iterations finished qdiffx linear iterations at : 22:35:06 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 7.6004426E-04 1.3595581E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 22:35:07 12.777u 0.194s 0:13.33 97.2% 0+0k 0+0io 0pf+0w