Mon Oct 10 13:59:59 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 Mon Oct 10 2011 at 13:59:59 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4235 !!! WARNING: HIR 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5916079 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): -24.96400 35.21100 ymin,ymax (A): 34.83800 92.33500 zmin,zma (A): 30.82600 89.67800 x,y,z range (A): 60.17500 57.49700 58.85200 scale (grids/A): 0.5916079 object centre (A): 5.123500 63.58650 60.25200 number of atom coordinates read : 4235 total number of charged atoms : 4099 net assigned charge : 1.4041901E-02 assigned positive charge : 639.7266 centred at (gu) : 90.88017 89.56326 88.66689 assigned negative charge : -639.7155 centred at (gu) : 90.69810 89.67776 88.85950 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9479 nv = 96 ne = 84 npr = 89296 no. pairs analyzed = 89296 no. exposed pairs = 4768 no. arc points = 32149 no. surface atoms = 1619 nbur = 2616 mkacc time = 0.2400000 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 = 1.484000 m= 467 mr = 5587 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 0.5200000 number of dielectric boundary points 4303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3430 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 12468 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1602881E-08 -6.8250308E-09 midg,1,midg; midg,igrid,midg 5.5345208E-09 -5.0298419E-09 1,midg,midg; igrid,midg,midg -7.1649673E-09 9.8479527E-09 gauss-seidel spectral radius is 0.9853376 estimated iterations to convergence 68 setup time was (sec) 1.000000 now iterating at: 14:00:01 rms-change max change #iterations 0.1346028 17.06712 at 10iterations 1.1575635E-02 1.425968 at 20iterations 1.2781848E-03 0.1531525 at 30iterations 2.8606335E-04 3.1105042E-02 at 40iterations 9.4978393E-05 1.1732817E-02 at 50iterations finished qdiffx linear iterations at : 14:00:08 total time elapsed so far: 8.020000 # loops : 50 mean,max change (kT/e) : 9.4978393E-05 1.1732817E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 14:00:08 8.191u 0.743s 0:09.45 94.4% 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 10 2011 at 14:00:09 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4235 !!! WARNING: HIR 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.774824 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): -24.96400 35.21100 ymin,ymax (A): 34.83800 92.33500 zmin,zma (A): 30.82600 89.67800 x,y,z range (A): 60.17500 57.49700 58.85200 scale (grids/A): 1.774824 object centre (A): 5.123500 63.58650 60.25200 number of atom coordinates read : 4235 total number of charged atoms : 4099 net assigned charge : 1.4041901E-02 assigned positive charge : 639.7266 centred at (gu) : 92.63921 88.68847 85.99944 assigned negative charge : -639.7155 centred at (gu) : 92.09380 89.03289 86.57794 start vw surface at 0.1700000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 105442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32149 grid for indexing accessible points = 1.400000 m= 36571 mr = 76978 m= 4958 mr = 27235 m= 236 mr = 3175 m= 0 mr = 83 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 7019 time to turn everything in is 0.9900000 number of dielectric boundary points 39736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 31935 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) : 0.5916079 object centre at (A) : 5.123500 63.58650 60.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9541982E-02 -3.9611772E-02 midg,1,midg; midg,igrid,midg 2.7710954E-02 -2.5723975E-02 1,midg,midg; igrid,midg,midg -1.1514443E-02 5.3711005E-02 gauss-seidel spectral radius is 0.9985749 estimated iterations to convergence 210 setup time was (sec) 1.540000 now iterating at: 14:00:12 rms-change max change #iterations 4.931154 236.2214 at 10iterations 2.265845 62.50559 at 20iterations 1.045435 29.40622 at 30iterations 0.4817947 13.49323 at 40iterations 0.2229832 5.976040 at 50iterations 0.1029837 2.900265 at 60iterations 4.7630865E-02 1.286037 at 70iterations 2.1962091E-02 0.5888062 at 80iterations 1.0196364E-02 0.2795711 at 90iterations 4.7353827E-03 0.1266103 at 100iterations 2.2198723E-03 6.2200546E-02 at 110iterations 1.0579062E-03 2.9914856E-02 at 120iterations finished qdiffx linear iterations at : 14:00:28 total time elapsed so far: 17.52000 # loops : 120 mean,max change (kT/e) : 1.0579062E-03 2.9914856E-02 energy calculations done at 17.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.70000 DelPhi exited at 14:00:29 17.706u 0.801s 0:19.93 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 Mon Oct 10 2011 at 14:00:30 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4235 !!! WARNING: HIR 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.662235 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): -24.96400 35.21100 ymin,ymax (A): 34.83800 92.33500 zmin,zma (A): 30.82600 89.67800 x,y,z range (A): 60.17500 57.49700 58.85200 scale (grids/A): 2.662235 object centre (A): 5.123500 63.58650 60.25200 number of atom coordinates read : 4235 total number of charged atoms : 4099 net assigned charge : 1.4041901E-02 assigned positive charge : 639.7266 centred at (gu) : 93.95873 88.03219 83.99892 assigned negative charge : -639.7155 centred at (gu) : 93.14066 88.54919 84.86681 start vw surface at 0.1600000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 245032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32149 grid for indexing accessible points = 1.400000 m= 122566 mr = 186422 m= 40190 mr = 101685 m= 8767 mr = 32415 m= 1082 mr = 6832 m= 25 mr = 708 m= 0 mr = 0 time to grow re-entrant surface = 1.510000 no. cavity mid-points inaccessible to solvent = 23383 time to turn everything in is 2.430000 number of dielectric boundary points 89600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.680000 number of grid points assigned charge 32783 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) : 1.774824 object centre at (A) : 5.123500 63.58650 60.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8705299 -0.4841705 midg,1,midg; midg,igrid,midg 0.3176645 -0.2387574 1,midg,midg; igrid,midg,midg 8.8232182E-02 0.4526291 gauss-seidel spectral radius is 0.9992664 estimated iterations to convergence 291 setup time was (sec) 2.990000 now iterating at: 14:00:34 rms-change max change #iterations 11.85562 303.0092 at 10iterations 6.997958 165.5988 at 20iterations 4.089912 76.42022 at 30iterations 2.387839 64.17027 at 40iterations 1.392649 24.95193 at 50iterations 0.8077300 14.16334 at 60iterations 0.4678576 7.664469 at 70iterations 0.2711815 4.182749 at 80iterations 0.1568904 2.840750 at 90iterations 9.0755858E-02 1.419097 at 100iterations 5.2436478E-02 0.8871489 at 110iterations 3.0310540E-02 0.4957539 at 120iterations 1.7559344E-02 0.2580414 at 130iterations 1.0154512E-02 0.1722202 at 140iterations 5.9255110E-03 8.7568283E-02 at 150iterations 3.4687552E-03 5.5466652E-02 at 160iterations 2.0579805E-03 3.2161713E-02 at 170iterations 1.2466265E-03 2.0204544E-02 at 180iterations finished qdiffx linear iterations at : 14:01:01 total time elapsed so far: 29.94000 # loops : 180 mean,max change (kT/e) : 1.2466265E-03 2.0204544E-02 energy calculations done at 29.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.13000 DelPhi exited at 14:01:02 30.139u 0.757s 0:31.90 96.8% 0+0k 0+0io 0pf+0w