Mon Oct 10 17:03:28 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 17:03:29 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2967 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5341817 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): -32.09600 34.54800 ymin,ymax (A): -25.37300 21.09100 zmin,zma (A): -40.64500 7.092000 x,y,z range (A): 66.64400 46.46400 47.73700 scale (grids/A): 0.5341817 object centre (A): 1.226000 -2.141000 -16.77650 number of atom coordinates read : 2967 total number of charged atoms : 2825 net assigned charge : -3.471963 assigned positive charge : 447.8890 centred at (gu) : 90.83291 89.91583 90.63495 assigned negative charge : -451.3620 centred at (gu) : 90.85371 90.07910 90.74174 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5447 nv = 96 ne = 84 npr = 59150 no. pairs analyzed = 59150 no. exposed pairs = 3849 no. arc points = 27335 no. surface atoms = 1301 nbur = 1666 mkacc time = 0.1600000 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 = 1.624000 m= 232 mr = 2710 m= 0 mr = 11 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3700000 number of dielectric boundary points 2958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2799 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7285532E-10 -7.0024381E-10 midg,1,midg; midg,igrid,midg 5.6853522E-10 -8.2857210E-10 1,midg,midg; igrid,midg,midg -3.4497880E-11 -2.7116243E-10 gauss-seidel spectral radius is 0.9819447 estimated iterations to convergence 61 setup time was (sec) 0.6400000 now iterating at: 17:03:29 rms-change max change #iterations 6.6531964E-02 13.20958 at 10iterations 4.1166209E-03 0.8107533 at 20iterations 2.6200700E-04 4.5848846E-02 at 30iterations 1.6495722E-05 2.5405884E-03 at 40iterations 1.0947656E-06 2.0980835E-04 at 50iterations finished qdiffx linear iterations at : 17:03:33 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 1.0947656E-06 2.0980835E-04 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 17:03:34 4.155u 0.282s 0:04.98 88.9% 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 17:03:34 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2967 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.602545 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): -32.09600 34.54800 ymin,ymax (A): -25.37300 21.09100 zmin,zma (A): -40.64500 7.092000 x,y,z range (A): 66.64400 46.46400 47.73700 scale (grids/A): 1.602545 object centre (A): 1.226000 -2.141000 -16.77650 number of atom coordinates read : 2967 total number of charged atoms : 2825 net assigned charge : -3.471963 assigned positive charge : 447.8890 centred at (gu) : 92.49801 89.74683 91.90414 assigned negative charge : -451.3620 centred at (gu) : 92.56068 90.23707 92.22478 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 61227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27335 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 17324 mr = 40595 m= 1493 mr = 11377 m= 38 mr = 652 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1084 time to turn everything in is 0.5600000 number of dielectric boundary points 27458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 21581 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) : 0.5341817 object centre at (A) : 1.226000 -2.141000 -16.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7801354E-03 -4.1805408E-03 midg,1,midg; midg,igrid,midg 6.4892052E-03 -1.3130835E-02 1,midg,midg; igrid,midg,midg -2.9568030E-03 -2.4582313E-02 gauss-seidel spectral radius is 0.9981143 estimated iterations to convergence 183 setup time was (sec) 0.8700000 now iterating at: 17:03:35 rms-change max change #iterations 3.214741 162.0780 at 10iterations 1.312953 58.02008 at 20iterations 0.5376079 20.79992 at 30iterations 0.2195745 8.309262 at 40iterations 8.9751437E-02 3.242220 at 50iterations 3.6787786E-02 1.510670 at 60iterations 1.5083132E-02 0.5687981 at 70iterations 6.1929892E-03 0.2285042 at 80iterations 2.5330447E-03 9.9314690E-02 at 90iterations 1.0418030E-03 3.7296891E-02 at 100iterations 4.2477337E-04 1.7231941E-02 at 110iterations 1.7433663E-04 6.4239502E-03 at 120iterations finished qdiffx linear iterations at : 17:03:43 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 1.7433663E-04 6.4239502E-03 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 17:03:44 9.361u 0.299s 0:10.20 94.6% 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 17:03:44 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2967 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.403817 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): -32.09600 34.54800 ymin,ymax (A): -25.37300 21.09100 zmin,zma (A): -40.64500 7.092000 x,y,z range (A): 66.64400 46.46400 47.73700 scale (grids/A): 2.403817 object centre (A): 1.226000 -2.141000 -16.77650 number of atom coordinates read : 2967 total number of charged atoms : 2825 net assigned charge : -3.471963 assigned positive charge : 447.8890 centred at (gu) : 93.74684 89.62000 92.85606 assigned negative charge : -451.3620 centred at (gu) : 93.84087 90.35558 93.33694 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 142527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27335 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 61483 mr = 99691 m= 15722 mr = 47596 m= 2186 mr = 11301 m= 138 mr = 1341 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 3287 time to turn everything in is 1.340000 number of dielectric boundary points 62070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 22567 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) : 1.602545 object centre at (A) : 1.226000 -2.141000 -16.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4583523E-02 -4.5608558E-02 midg,1,midg; midg,igrid,midg 0.1176590 -0.1840852 1,midg,midg; igrid,midg,midg 7.9958811E-02 -0.7784190 gauss-seidel spectral radius is 0.9991190 estimated iterations to convergence 266 setup time was (sec) 1.660000 now iterating at: 17:03:46 rms-change max change #iterations 8.484412 270.5120 at 10iterations 4.710406 136.6869 at 20iterations 2.608525 75.09059 at 30iterations 1.432577 36.54702 at 40iterations 0.7882376 17.79622 at 50iterations 0.4322031 9.764397 at 60iterations 0.2361310 4.918489 at 70iterations 0.1289675 2.588999 at 80iterations 7.0248052E-02 1.526289 at 90iterations 3.8429264E-02 0.8815864 at 100iterations 2.0962460E-02 0.4607691 at 110iterations 1.1422139E-02 0.2389545 at 120iterations 6.2388047E-03 0.1359253 at 130iterations 3.3989672E-03 7.2204590E-02 at 140iterations 1.8516397E-03 4.2402267E-02 at 150iterations 1.0103205E-03 2.3515701E-02 at 160iterations 5.5151241E-04 1.1344910E-02 at 170iterations 3.0016812E-04 6.0043335E-03 at 180iterations finished qdiffx linear iterations at : 17:03:59 total time elapsed so far: 15.13000 # loops : 180 mean,max change (kT/e) : 3.0016812E-04 6.0043335E-03 energy calculations done at 15.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.32000 DelPhi exited at 17:04:01 15.320u 0.301s 0:16.86 92.6% 0+0k 0+0io 0pf+0w