Mon Oct 31 18:26:35 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 Mon Oct 31 2011 at 18:26:35 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 ! Automatically converted by prot2crg.py # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5767330 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 0.5767330 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3062 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 459.7828 centred at (gu) : 91.10113 89.94644 90.15296 assigned negative charge : -457.5339 centred at (gu) : 91.22202 89.92796 90.26438 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6667 nv = 96 ne = 84 npr = 62105 no. pairs analyzed = 62105 no. exposed pairs = 3808 no. arc points = 26828 no. surface atoms = 1277 nbur = 1785 mkacc time = 9.9999994E-02 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 = 1.512000 m= 307 mr = 3625 m= 3 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2752 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6107991E-09 -1.8854243E-09 midg,1,midg; midg,igrid,midg 1.0051684E-10 8.3943869E-10 1,midg,midg; igrid,midg,midg 2.2315063E-09 -2.6354541E-09 gauss-seidel spectral radius is 0.9844903 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 18:26:35 rms-change max change #iterations 9.7184703E-02 15.67820 at 10iterations 7.8243688E-03 1.231525 at 20iterations 1.1514062E-03 0.2358913 at 30iterations 4.3631293E-04 9.9046707E-02 at 40iterations 1.9142398E-04 4.3474197E-02 at 50iterations finished qdiffx linear iterations at : 18:26:39 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 1.9142398E-04 4.3474197E-02 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.850000 DelPhi exited at 18:26:39 3.856u 0.196s 0:04.69 86.1% 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 Mon Oct 31 2011 at 18:26:39 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 ! Automatically converted by prot2crg.py # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.730199 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 1.730199 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3062 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 459.7828 centred at (gu) : 93.30260 89.83813 90.45805 assigned negative charge : -457.5339 centred at (gu) : 93.66559 89.78358 90.79282 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 74183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26828 grid for indexing accessible points = 1.400000 m= 23642 mr = 51434 m= 2736 mr = 16701 m= 89 mr = 1483 m= 0 mr = 9 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1038 time to turn everything in is 0.3400000 number of dielectric boundary points 31023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 266 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 22596 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) : 0.5767330 object centre at (A) : 1.770501 -0.7205009 22.12450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3355050E-02 2.0000197E-02 midg,1,midg; midg,igrid,midg -3.6597205E-04 1.7384983E-03 1,midg,midg; igrid,midg,midg 4.0768357E-03 -8.5937995E-03 gauss-seidel spectral radius is 0.9984012 estimated iterations to convergence 198 setup time was (sec) 0.5900000 now iterating at: 18:26:41 rms-change max change #iterations 3.832006 188.5269 at 10iterations 1.677705 54.41395 at 20iterations 0.7382224 26.90773 at 30iterations 0.3244523 11.04586 at 40iterations 0.1432566 5.118664 at 50iterations 6.3091420E-02 2.043611 at 60iterations 2.7905215E-02 0.9395485 at 70iterations 1.2452126E-02 0.4128523 at 80iterations 5.7183509E-03 0.2487106 at 90iterations 2.8259386E-03 0.1149445 at 100iterations 1.5670832E-03 6.3385010E-02 at 110iterations 1.0027374E-03 4.3762207E-02 at 120iterations finished qdiffx linear iterations at : 18:26:49 total time elapsed so far: 8.400000 # loops : 120 mean,max change (kT/e) : 1.0027374E-03 4.3762207E-02 energy calculations done at 8.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.530000 DelPhi exited at 18:26:49 8.534u 0.295s 0:09.74 90.5% 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 Mon Oct 31 2011 at 18:26:49 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 ! Automatically converted by prot2crg.py # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.595299 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 2.595299 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3062 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 459.7828 centred at (gu) : 94.95368 89.75690 90.68674 assigned negative charge : -457.5339 centred at (gu) : 95.49839 89.67529 91.18927 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 172093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26828 grid for indexing accessible points = 1.400000 m= 81579 mr = 125208 m= 24383 mr = 65768 m= 4574 mr = 18707 m= 420 mr = 3139 m= 6 mr = 214 m= 0 mr = 3 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 3607 time to turn everything in is 0.9100000 number of dielectric boundary points 70016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 23298 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) : 1.730199 object centre at (A) : 1.770501 -0.7205009 22.12450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9182898E-02 0.5356284 midg,1,midg; midg,igrid,midg -6.5159560E-03 2.4737937E-02 1,midg,midg; igrid,midg,midg 1.8238341E-02 -9.5553458E-02 gauss-seidel spectral radius is 0.9992031 estimated iterations to convergence 280 setup time was (sec) 1.160000 now iterating at: 18:26:53 rms-change max change #iterations 9.462442 322.6792 at 10iterations 5.393294 130.2075 at 20iterations 3.084044 67.80568 at 30iterations 1.745642 40.24688 at 40iterations 0.9898131 21.94883 at 50iterations 0.5580243 11.38231 at 60iterations 0.3155565 6.353741 at 70iterations 0.1780366 3.334966 at 80iterations 0.1006458 2.144552 at 90iterations 5.6617897E-02 1.083133 at 100iterations 3.1999800E-02 0.5785186 at 110iterations 1.8113384E-02 0.3473125 at 120iterations 1.0321857E-02 0.2142887 at 130iterations 5.9786425E-03 0.1449509 at 140iterations 3.5626197E-03 8.1880569E-02 at 150iterations 2.2447621E-03 5.7769775E-02 at 160iterations 1.5183486E-03 3.7536621E-02 at 170iterations 1.1127890E-03 2.9664993E-02 at 180iterations finished qdiffx linear iterations at : 18:27:10 total time elapsed so far: 13.92000 # loops : 180 mean,max change (kT/e) : 1.1127890E-03 2.9664993E-02 energy calculations done at 13.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.05000 DelPhi exited at 18:27:11 14.054u 0.448s 0:21.38 67.7% 0+0k 0+0io 0pf+0w