Mon Oct 10 19:32:39 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 19:32:39 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 # of charge parameter records: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2856 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 has a net charge of 0.5140 !!! WARNING: TYR 271 has a net charge of -0.2720 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: 0.5620106 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): 1.906000 56.99900 ymin,ymax (A): -14.31500 34.70200 zmin,zma (A): 29.04300 92.38700 x,y,z range (A): 55.09300 49.01700 63.34400 scale (grids/A): 0.5620106 object centre (A): 29.45250 10.19350 60.71500 number of atom coordinates read : 2856 total number of charged atoms : 2717 net assigned charge : 9.256024 assigned positive charge : 427.3292 centred at (gu) : 88.49787 88.57800 91.11868 assigned negative charge : -418.0746 centred at (gu) : 88.59540 88.57977 91.23878 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5710 nv = 96 ne = 84 npr = 57812 no. pairs analyzed = 57812 no. exposed pairs = 3985 no. arc points = 27612 no. surface atoms = 1328 nbur = 1528 mkacc time = 0.1200000 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 = 1.540000 m= 263 mr = 2643 m= 3 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2765 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7450 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8146771E-09 -4.1639692E-10 midg,1,midg; midg,igrid,midg 1.5005664E-09 7.4385303E-10 1,midg,midg; igrid,midg,midg 3.0543019E-09 -1.7395287E-11 gauss-seidel spectral radius is 0.9836614 estimated iterations to convergence 64 setup time was (sec) 0.5300000 now iterating at: 19:32:40 rms-change max change #iterations 8.1145100E-02 12.75927 at 10iterations 6.0183895E-03 1.073223 at 20iterations 7.0164708E-04 0.1502514 at 30iterations 1.7779825E-04 4.7063828E-02 at 40iterations 5.5278360E-05 1.5064240E-02 at 50iterations finished qdiffx linear iterations at : 19:32:43 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 5.5278360E-05 1.5064240E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 19:32:43 3.260u 0.174s 0:03.88 88.4% 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 19:32:43 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2856 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 has a net charge of 0.5140 !!! WARNING: TYR 271 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.686032 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): 1.906000 56.99900 ymin,ymax (A): -14.31500 34.70200 zmin,zma (A): 29.04300 92.38700 x,y,z range (A): 55.09300 49.01700 63.34400 scale (grids/A): 1.686032 object centre (A): 29.45250 10.19350 60.71500 number of atom coordinates read : 2856 total number of charged atoms : 2717 net assigned charge : 9.256024 assigned positive charge : 427.3292 centred at (gu) : 85.49284 85.73292 93.35538 assigned negative charge : -418.0746 centred at (gu) : 85.78574 85.73906 93.71617 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27612 grid for indexing accessible points = 1.400000 m= 18687 mr = 39287 m= 2310 mr = 12108 m= 107 mr = 1080 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 30668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 249 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 20988 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) : 0.5620106 object centre at (A) : 29.45250 10.19350 60.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4289023E-02 -2.6772115E-02 midg,1,midg; midg,igrid,midg 1.2170943E-02 5.9647565E-03 1,midg,midg; igrid,midg,midg 1.8732859E-02 1.4988078E-02 gauss-seidel spectral radius is 0.9982854 estimated iterations to convergence 192 setup time was (sec) 0.7600000 now iterating at: 19:32:44 rms-change max change #iterations 3.437614 199.6217 at 10iterations 1.452308 60.70690 at 20iterations 0.6208178 23.58632 at 30iterations 0.2651491 9.860580 at 40iterations 0.1126427 3.971949 at 50iterations 4.8072577E-02 1.720406 at 60iterations 2.0540286E-02 0.8561363 at 70iterations 8.8650258E-03 0.3367996 at 80iterations 3.8346467E-03 0.1607742 at 90iterations 1.7116547E-03 7.1107864E-02 at 100iterations 7.9565012E-04 3.2111168E-02 at 110iterations 4.0643330E-04 1.9187927E-02 at 120iterations finished qdiffx linear iterations at : 19:32:51 total time elapsed so far: 7.150000 # loops : 120 mean,max change (kT/e) : 4.0643330E-04 1.9187927E-02 energy calculations done at 7.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 19:32:53 7.331u 0.240s 0:09.47 79.9% 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 19:32:53 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2856 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 has a net charge of 0.5140 !!! WARNING: TYR 271 has a net charge of -0.2720 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: 2.529048 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): 1.906000 56.99900 ymin,ymax (A): -14.31500 34.70200 zmin,zma (A): 29.04300 92.38700 x,y,z range (A): 55.09300 49.01700 63.34400 scale (grids/A): 2.529048 object centre (A): 29.45250 10.19350 60.71500 number of atom coordinates read : 2856 total number of charged atoms : 2717 net assigned charge : 9.256024 assigned positive charge : 427.3292 centred at (gu) : 83.23923 83.59915 95.03293 assigned negative charge : -418.0746 centred at (gu) : 83.67858 83.60860 95.57405 start vw surface at 0.1800000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 144116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27612 grid for indexing accessible points = 1.400000 m= 63023 mr = 97180 m= 19377 mr = 47540 m= 3516 mr = 14052 m= 303 mr = 2226 m= 7 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.090000 number of dielectric boundary points 69199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 21723 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) : 1.686032 object centre at (A) : 29.45250 10.19350 60.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4268387 -0.6190384 midg,1,midg; midg,igrid,midg 0.1900205 8.2638003E-02 1,midg,midg; igrid,midg,midg 0.2018277 0.3225754 gauss-seidel spectral radius is 0.9991637 estimated iterations to convergence 273 setup time was (sec) 1.400000 now iterating at: 19:32:54 rms-change max change #iterations 8.779840 336.7202 at 10iterations 4.978010 110.0125 at 20iterations 2.803950 67.35185 at 30iterations 1.577493 35.82777 at 40iterations 0.8820678 20.82945 at 50iterations 0.4942369 10.54691 at 60iterations 0.2753594 5.860729 at 70iterations 0.1532151 3.194303 at 80iterations 8.5282505E-02 2.022753 at 90iterations 4.7485594E-02 1.052276 at 100iterations 2.6467547E-02 0.5574379 at 110iterations 1.4708180E-02 0.3179550 at 120iterations 8.2223359E-03 0.1699314 at 130iterations 4.6271062E-03 9.8476410E-02 at 140iterations 2.6296207E-03 5.9606552E-02 at 150iterations 1.5217843E-03 3.5680771E-02 at 160iterations 9.1528811E-04 2.3700714E-02 at 170iterations 5.8050122E-04 1.6164780E-02 at 180iterations finished qdiffx linear iterations at : 19:33:04 total time elapsed so far: 11.28000 # loops : 180 mean,max change (kT/e) : 5.8050122E-04 1.6164780E-02 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 19:33:06 11.493u 0.195s 0:12.71 91.8% 0+0k 0+0io 0pf+0w