Tue Nov 22 14:18:46 PST 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 Tue Nov 22 2011 at 14:18:51 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6068975 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): -8.950000 49.70900 ymin,ymax (A): -19.05100 19.76600 zmin,zma (A): -7.735000 34.48900 x,y,z range (A): 58.65900 38.81700 42.22400 scale (grids/A): 0.6068975 object centre (A): 20.37950 0.3575001 13.37700 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.26814 90.35449 89.57840 assigned negative charge : -284.8263 centred at (gu) : 90.27121 90.45415 89.44261 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4847 nv = 96 ne = 84 npr = 40082 no. pairs analyzed = 40082 no. exposed pairs = 2504 no. arc points = 17505 no. surface atoms = 844 nbur = 1120 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 211 mr = 2612 m= 0 mr = 13 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1885 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5979 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2237022E-09 5.5189164E-09 midg,1,midg; midg,igrid,midg 4.5297508E-09 -1.8408042E-09 1,midg,midg; igrid,midg,midg 1.6474604E-09 1.6360194E-09 gauss-seidel spectral radius is 0.9858917 estimated iterations to convergence 69 setup time was (sec) 0.4400000 now iterating at: 14:18:54 rms-change max change #iterations 9.7305298E-02 17.19796 at 10iterations 8.3263023E-03 1.720095 at 20iterations 7.2618003E-04 0.1338692 at 30iterations 6.1758568E-05 1.0187387E-02 at 40iterations 5.4065081E-06 8.9097023E-04 at 50iterations finished qdiffx linear iterations at : 14:19:00 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 5.4065081E-06 8.9097023E-04 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 14:19:01 3.046u 0.131s 0:11.23 28.2% 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 Tue Nov 22 2011 at 14:19:04 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.820692 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): -8.950000 49.70900 ymin,ymax (A): -19.05100 19.76600 zmin,zma (A): -7.735000 34.48900 x,y,z range (A): 58.65900 38.81700 42.22400 scale (grids/A): 1.820692 object centre (A): 20.37950 0.3575001 13.37700 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.80444 91.06351 88.73496 assigned negative charge : -284.8263 centred at (gu) : 90.81385 91.36256 88.32800 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 52750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17505 grid for indexing accessible points = 1.400000 m= 17930 mr = 35890 m= 2248 mr = 13355 m= 79 mr = 1284 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1024 time to turn everything in is 0.3600000 number of dielectric boundary points 22454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 14332 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) : 0.6068975 object centre at (A) : 20.37950 0.3575001 13.37700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3520852E-03 1.1123270E-02 midg,1,midg; midg,igrid,midg 5.0680032E-03 -3.9422959E-03 1,midg,midg; igrid,midg,midg 3.2528546E-02 2.9279681E-02 gauss-seidel spectral radius is 0.9984307 estimated iterations to convergence 200 setup time was (sec) 0.6200000 now iterating at: 14:19:08 rms-change max change #iterations 3.254145 191.1752 at 10iterations 1.436190 61.51005 at 20iterations 0.6366656 26.86682 at 30iterations 0.2813707 12.22481 at 40iterations 0.1252357 4.869545 at 50iterations 5.5663329E-02 2.036018 at 60iterations 2.4507940E-02 0.8976974 at 70iterations 1.0859962E-02 0.4685974 at 80iterations 4.8149982E-03 0.1751747 at 90iterations 2.1368484E-03 8.3902359E-02 at 100iterations 9.4309886E-04 3.4033775E-02 at 110iterations 4.1956003E-04 1.5328884E-02 at 120iterations finished qdiffx linear iterations at : 14:19:26 total time elapsed so far: 6.550000 # loops : 120 mean,max change (kT/e) : 4.1956003E-04 1.5328884E-02 energy calculations done at 6.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.720000 DelPhi exited at 14:19:28 6.726u 0.135s 0:24.40 28.0% 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 Tue Nov 22 2011 at 14:19:29 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.731039 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): -8.950000 49.70900 ymin,ymax (A): -19.05100 19.76600 zmin,zma (A): -7.735000 34.48900 x,y,z range (A): 58.65900 38.81700 42.22400 scale (grids/A): 2.731039 object centre (A): 20.37950 0.3575001 13.37700 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.20679 91.59534 88.10249 assigned negative charge : -284.8263 centred at (gu) : 91.22084 92.04379 87.49208 start vw surface at 0.1100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 121972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17505 grid for indexing accessible points = 1.400000 m= 59694 mr = 87000 m= 19763 mr = 48962 m= 3719 mr = 15962 m= 335 mr = 2667 m= 14 mr = 198 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 3447 time to turn everything in is 0.8700000 number of dielectric boundary points 50706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 14651 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) : 1.820692 object centre at (A) : 20.37950 0.3575001 13.37700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3068062E-02 9.7397849E-02 midg,1,midg; midg,igrid,midg 3.3233862E-02 -3.5784364E-02 1,midg,midg; igrid,midg,midg 0.3397971 0.3319605 gauss-seidel spectral radius is 0.9991847 estimated iterations to convergence 277 setup time was (sec) 1.150000 now iterating at: 14:19:36 rms-change max change #iterations 7.755580 297.8658 at 10iterations 4.390133 126.2557 at 20iterations 2.468652 62.86231 at 30iterations 1.380373 32.63730 at 40iterations 0.7705052 17.85891 at 50iterations 0.4300327 9.442655 at 60iterations 0.2394565 5.831604 at 70iterations 0.1333056 2.796219 at 80iterations 7.4447490E-02 1.530884 at 90iterations 4.1517615E-02 0.9205527 at 100iterations 2.3078980E-02 0.4764147 at 110iterations 1.2903337E-02 0.2797699 at 120iterations 7.1948296E-03 0.1662035 at 130iterations 4.0094657E-03 9.1777802E-02 at 140iterations 2.2342347E-03 4.9488544E-02 at 150iterations 1.2418377E-03 2.7141094E-02 at 160iterations 6.9268094E-04 1.3698578E-02 at 170iterations 3.8716450E-04 7.8799725E-03 at 180iterations finished qdiffx linear iterations at : 14:20:07 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 3.8716450E-04 7.8799725E-03 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.71000 DelPhi exited at 14:20:09 11.708u 0.154s 0:40.08 29.5% 0+0k 0+0io 0pf+0w