Mon Oct 10 17:14:51 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 17:14:51 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2858 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: 0.5443009 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): -6.868000 40.41100 ymin,ymax (A): -9.372000 42.00800 zmin,zma (A): -3.315000 62.09000 x,y,z range (A): 47.27900 51.38000 65.40500 scale (grids/A): 0.5443009 object centre (A): 16.77150 16.31800 29.38750 number of atom coordinates read : 2858 total number of charged atoms : 2716 net assigned charge : 1.000033 assigned positive charge : 423.9873 centred at (gu) : 90.25926 89.47949 89.58969 assigned negative charge : -422.9884 centred at (gu) : 90.19646 89.42738 89.64208 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5532 nv = 96 ne = 84 npr = 56995 no. pairs analyzed = 56995 no. exposed pairs = 3755 no. arc points = 26583 no. surface atoms = 1264 nbur = 1594 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 = 1.568000 m= 222 mr = 2772 m= 2 mr = 12 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 0.2200000 number of dielectric boundary points 2972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2623 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7192 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0681727E-10 -2.3003947E-10 midg,1,midg; midg,igrid,midg -2.8987540E-10 3.2074257E-10 1,midg,midg; igrid,midg,midg -2.9779193E-10 4.5667195E-10 gauss-seidel spectral radius is 0.9825937 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 17:14:52 rms-change max change #iterations 7.0537634E-02 11.72784 at 10iterations 4.6625407E-03 0.8561082 at 20iterations 3.3664508E-04 5.9864044E-02 at 30iterations 2.9733366E-05 5.9967041E-03 at 40iterations 3.8328280E-06 7.6484680E-04 at 50iterations finished qdiffx linear iterations at : 17:14:55 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 3.8328280E-06 7.6484680E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 17:14:55 3.452u 0.162s 0:03.93 91.8% 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 17:14:55 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2858 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: 1.632903 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): -6.868000 40.41100 ymin,ymax (A): -9.372000 42.00800 zmin,zma (A): -3.315000 62.09000 x,y,z range (A): 47.27900 51.38000 65.40500 scale (grids/A): 1.632903 object centre (A): 16.77150 16.31800 29.38750 number of atom coordinates read : 2858 total number of charged atoms : 2716 net assigned charge : 1.000033 assigned positive charge : 423.9873 centred at (gu) : 90.77728 88.43769 88.76840 assigned negative charge : -422.9884 centred at (gu) : 90.58908 88.28208 88.92600 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 60781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26583 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18886 mr = 40108 m= 1967 mr = 12959 m= 58 mr = 963 m= 0 mr = 9 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 294 time to turn everything in is 0.3200000 number of dielectric boundary points 27653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 20756 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) : 0.5443009 object centre at (A) : 16.77150 16.31800 29.38750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5083131E-02 1.1410099E-02 midg,1,midg; midg,igrid,midg -9.9241817E-03 -1.9585285E-03 1,midg,midg; igrid,midg,midg -2.5922121E-03 1.5926661E-03 gauss-seidel spectral radius is 0.9981784 estimated iterations to convergence 186 setup time was (sec) 0.5400000 now iterating at: 17:14:56 rms-change max change #iterations 3.196245 185.4012 at 10iterations 1.324992 52.72253 at 20iterations 0.5524499 22.23090 at 30iterations 0.2289820 8.918714 at 40iterations 9.5263578E-02 3.433671 at 50iterations 3.9692853E-02 1.550709 at 60iterations 1.6468100E-02 0.5737457 at 70iterations 6.8667429E-03 0.2621574 at 80iterations 2.8606153E-03 0.1029644 at 90iterations 1.1928984E-03 4.4776917E-02 at 100iterations 4.9676717E-04 1.7377853E-02 at 110iterations 2.0753608E-04 7.8825951E-03 at 120iterations finished qdiffx linear iterations at : 17:15:03 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.0753608E-04 7.8825951E-03 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 17:15:04 7.757u 0.193s 0:08.35 95.0% 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 Mon Oct 10 2011 at 17:15:04 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2858 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: 2.449354 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): -6.868000 40.41100 ymin,ymax (A): -9.372000 42.00800 zmin,zma (A): -3.315000 62.09000 x,y,z range (A): 47.27900 51.38000 65.40500 scale (grids/A): 2.449354 object centre (A): 16.77150 16.31800 29.38750 number of atom coordinates read : 2858 total number of charged atoms : 2716 net assigned charge : 1.000033 assigned positive charge : 423.9873 centred at (gu) : 91.16577 87.65620 88.15244 assigned negative charge : -422.9884 centred at (gu) : 90.88350 87.42310 88.38896 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 141132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26583 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 64597 mr = 98466 m= 18706 mr = 50618 m= 3029 mr = 14101 m= 169 mr = 1997 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1009 time to turn everything in is 0.7400000 number of dielectric boundary points 62389 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 21704 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) : 1.632903 object centre at (A) : 16.77150 16.31800 29.38750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1477393 0.4404677 midg,1,midg; midg,igrid,midg -0.1048486 -5.9087772E-02 1,midg,midg; igrid,midg,midg -3.5099130E-02 1.6669974E-02 gauss-seidel spectral radius is 0.9991395 estimated iterations to convergence 269 setup time was (sec) 0.9700000 now iterating at: 17:15:05 rms-change max change #iterations 8.423360 346.1692 at 10iterations 4.754283 113.4068 at 20iterations 2.657774 68.36411 at 30iterations 1.480464 43.90162 at 40iterations 0.8238176 21.30944 at 50iterations 0.4552130 9.850857 at 60iterations 0.2519713 6.452845 at 70iterations 0.1390904 3.257977 at 80iterations 7.6617658E-02 1.536759 at 90iterations 4.2142499E-02 0.9138374 at 100iterations 2.3154568E-02 0.5003052 at 110iterations 1.2793036E-02 0.2654686 at 120iterations 7.0251357E-03 0.1640778 at 130iterations 3.8633051E-03 7.8983307E-02 at 140iterations 2.1263740E-03 4.3884277E-02 at 150iterations 1.1691333E-03 2.5618553E-02 at 160iterations 6.4128044E-04 1.3993025E-02 at 170iterations 3.5425296E-04 7.6065063E-03 at 180iterations finished qdiffx linear iterations at : 17:15:16 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 3.5425296E-04 7.6065063E-03 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.35000 DelPhi exited at 17:15:16 12.349u 0.194s 0:12.84 97.5% 0+0k 0+0io 0pf+0w