Sat Oct 8 11:37:14 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 Sat Oct 8 2011 at 11:37:14 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: ZN5 522 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6323044 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): 32.08200 81.47400 ymin,ymax (A): 25.28900 81.59100 zmin,zma (A): -2.982000 46.36000 x,y,z range (A): 49.39200 56.30199 49.34200 scale (grids/A): 0.6323044 object centre (A): 56.77800 53.44000 21.68900 number of atom coordinates read : 3338 total number of charged atoms : 3187 net assigned charge : -2.699966 assigned positive charge : 508.9884 centred at (gu) : 90.84222 89.61491 91.08405 assigned negative charge : -511.6895 centred at (gu) : 90.62471 89.71389 91.06524 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8632 nv = 96 ne = 84 npr = 70868 no. pairs analyzed = 70868 no. exposed pairs = 3615 no. arc points = 24601 no. surface atoms = 1242 nbur = 2096 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 5235 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3600000 number of dielectric boundary points 3820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2491 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5868433E-09 -1.3533888E-09 midg,1,midg; midg,igrid,midg 9.5187094E-09 -1.4590859E-08 1,midg,midg; igrid,midg,midg -2.5885761E-08 2.7695538E-08 gauss-seidel spectral radius is 0.9870937 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 11:37:15 rms-change max change #iterations 0.1632106 23.91775 at 10iterations 1.5850060E-02 1.981210 at 20iterations 1.5411208E-03 0.1868896 at 30iterations 1.5230557E-04 1.9878387E-02 at 40iterations 1.5399499E-05 1.8882751E-03 at 50iterations finished qdiffx linear iterations at : 11:37:18 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 1.5399499E-05 1.8882751E-03 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 11:37:19 3.894u 0.234s 0:04.64 88.7% 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 Sat Oct 8 2011 at 11:37:19 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: ZN5 522 has a net charge of 1.4000 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: 1.896913 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): 32.08200 81.47400 ymin,ymax (A): 25.28900 81.59100 zmin,zma (A): -2.982000 46.36000 x,y,z range (A): 49.39200 56.30199 49.34200 scale (grids/A): 1.896913 object centre (A): 56.77800 53.44000 21.68900 number of atom coordinates read : 3338 total number of charged atoms : 3187 net assigned charge : -2.699966 assigned positive charge : 508.9884 centred at (gu) : 92.52582 88.84354 93.25099 assigned negative charge : -511.6895 centred at (gu) : 91.87333 89.14124 93.19524 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 93883 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24601 grid for indexing accessible points = 1.400000 m= 36978 mr = 68929 m= 6196 mr = 29082 m= 325 mr = 4216 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1218 time to turn everything in is 0.6700000 number of dielectric boundary points 35057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 25071 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) : 0.6323044 object centre at (A) : 56.77800 53.44000 21.68900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5747741E-02 -2.7582161E-02 midg,1,midg; midg,igrid,midg 7.5954353E-03 -3.0111723E-02 1,midg,midg; igrid,midg,midg -3.8353570E-02 3.5873741E-02 gauss-seidel spectral radius is 0.9986776 estimated iterations to convergence 218 setup time was (sec) 1.000000 now iterating at: 11:37:20 rms-change max change #iterations 4.928254 183.7687 at 10iterations 2.336052 74.95262 at 20iterations 1.109758 31.48641 at 30iterations 0.5277649 15.68326 at 40iterations 0.2502735 7.125536 at 50iterations 0.1193929 3.285210 at 60iterations 5.6415875E-02 1.452180 at 70iterations 2.6859950E-02 0.8046169 at 80iterations 1.2758310E-02 0.3716698 at 90iterations 6.0522812E-03 0.1900835 at 100iterations 2.8888639E-03 7.9220772E-02 at 110iterations 1.3732103E-03 3.6748886E-02 at 120iterations finished qdiffx linear iterations at : 11:37:30 total time elapsed so far: 10.40000 # loops : 120 mean,max change (kT/e) : 1.3732103E-03 3.6748886E-02 energy calculations done at 10.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.58000 DelPhi exited at 11:37:31 10.581u 0.282s 0:11.41 95.1% 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 11:37:31 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: ZN5 522 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.845370 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): 32.08200 81.47400 ymin,ymax (A): 25.28900 81.59100 zmin,zma (A): -2.982000 46.36000 x,y,z range (A): 49.39200 56.30199 49.34200 scale (grids/A): 2.845370 object centre (A): 56.77800 53.44000 21.68900 number of atom coordinates read : 3338 total number of charged atoms : 3187 net assigned charge : -2.699966 assigned positive charge : 508.9884 centred at (gu) : 93.78854 88.26530 94.87640 assigned negative charge : -511.6895 centred at (gu) : 92.80971 88.71198 94.79279 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 217304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24601 grid for indexing accessible points = 1.400000 m= 117126 mr = 165925 m= 45930 mr = 99489 m= 11428 mr = 38894 m= 1449 mr = 8979 m= 61 mr = 963 m= 0 mr = 13 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 4133 time to turn everything in is 1.750000 number of dielectric boundary points 79035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 25496 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) : 1.896913 object centre at (A) : 56.77800 53.44000 21.68900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1864356 -0.2751271 midg,1,midg; midg,igrid,midg 0.1762541 0.1483787 1,midg,midg; igrid,midg,midg -0.3797302 0.4225413 gauss-seidel spectral radius is 0.9992721 estimated iterations to convergence 292 setup time was (sec) 2.100000 now iterating at: 11:37:33 rms-change max change #iterations 11.43331 337.3458 at 10iterations 6.694517 122.5575 at 20iterations 3.894541 71.27045 at 30iterations 2.263354 38.47739 at 40iterations 1.315997 22.83578 at 50iterations 0.7609384 11.73002 at 60iterations 0.4414704 6.806334 at 70iterations 0.2548400 3.852937 at 80iterations 0.1476038 2.341652 at 90iterations 8.5159995E-02 1.566738 at 100iterations 4.9209759E-02 0.7901421 at 110iterations 2.8422860E-02 0.4495926 at 120iterations 1.6460765E-02 0.2732811 at 130iterations 9.5047532E-03 0.1468277 at 140iterations 5.4880632E-03 8.9535713E-02 at 150iterations 3.1696942E-03 5.1290512E-02 at 160iterations 1.8336289E-03 3.0685425E-02 at 170iterations 1.0610404E-03 1.7181396E-02 at 180iterations finished qdiffx linear iterations at : 11:37:46 total time elapsed so far: 14.89000 # loops : 180 mean,max change (kT/e) : 1.0610404E-03 1.7181396E-02 energy calculations done at 14.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.06000 DelPhi exited at 11:37:46 15.058u 0.290s 0:15.74 97.4% 0+0k 0+0io 0pf+0w