Tue Oct 11 04:31:54 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+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 Oct 11 2011 at 04:31:54 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6374217 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): -11.30900 36.30000 ymin,ymax (A): -25.82900 22.50000 zmin,zma (A): -10.44400 45.40600 x,y,z range (A): 47.60900 48.32900 55.85000 scale (grids/A): 0.6374217 object centre (A): 12.49550 -1.664500 17.48100 number of atom coordinates read : 2769 total number of charged atoms : 2616 net assigned charge : 2.140015 assigned positive charge : 417.9576 centred at (gu) : 90.13721 90.46303 92.05344 assigned negative charge : -415.8183 centred at (gu) : 89.89812 90.32968 91.98240 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7322 nv = 96 ne = 84 npr = 57051 no. pairs analyzed = 57051 no. exposed pairs = 3336 no. arc points = 23210 no. surface atoms = 1124 nbur = 1645 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 4110 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2296 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8977 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6014616E-09 1.6908309E-08 midg,1,midg; midg,igrid,midg -1.1803302E-08 1.9752022E-08 1,midg,midg; igrid,midg,midg -2.5082562E-08 3.0533069E-08 gauss-seidel spectral radius is 0.9872580 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 04:31:54 rms-change max change #iterations 0.1471757 19.35045 at 10iterations 1.4719834E-02 1.840576 at 20iterations 1.5101148E-03 0.1965103 at 30iterations 1.7409869E-04 2.9520035E-02 at 40iterations 2.8362872E-05 4.2743683E-03 at 50iterations finished qdiffx linear iterations at : 04:31:57 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.8362872E-05 4.2743683E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 04:31:58 3.352u 0.175s 0:03.81 92.3% 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 Oct 11 2011 at 04:31:58 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.912265 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): -11.30900 36.30000 ymin,ymax (A): -25.82900 22.50000 zmin,zma (A): -10.44400 45.40600 x,y,z range (A): 47.60900 48.32900 55.85000 scale (grids/A): 1.912265 object centre (A): 12.49550 -1.664500 17.48100 number of atom coordinates read : 2769 total number of charged atoms : 2616 net assigned charge : 2.140015 assigned positive charge : 417.9576 centred at (gu) : 90.41110 91.38812 96.15975 assigned negative charge : -415.8183 centred at (gu) : 89.69405 90.98871 95.94694 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23210 grid for indexing accessible points = 1.400000 m= 28919 mr = 55957 m= 4496 mr = 21515 m= 280 mr = 2863 m= 5 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1688 time to turn everything in is 0.3900000 number of dielectric boundary points 32848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20568 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) : 0.6374217 object centre at (A) : 12.49550 -1.664500 17.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3255666E-02 1.6176371E-02 midg,1,midg; midg,igrid,midg -1.2370581E-02 1.3185076E-02 1,midg,midg; igrid,midg,midg -1.3602953E-02 5.3407095E-02 gauss-seidel spectral radius is 0.9986587 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 04:31:59 rms-change max change #iterations 4.442745 205.9701 at 10iterations 2.094894 76.23943 at 20iterations 0.9915093 32.30906 at 30iterations 0.4676660 15.63932 at 40iterations 0.2207537 7.848664 at 50iterations 0.1039508 3.288803 at 60iterations 4.9289893E-02 1.482290 at 70iterations 2.3260122E-02 0.8430452 at 80iterations 1.0992680E-02 0.3071564 at 90iterations 5.1931650E-03 0.1553955 at 100iterations 2.4532326E-03 7.2792053E-02 at 110iterations 1.1685883E-03 3.6116362E-02 at 120iterations finished qdiffx linear iterations at : 04:32:06 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.1685883E-03 3.6116362E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 04:32:06 7.737u 0.195s 0:08.34 94.9% 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 Tue Oct 11 2011 at 04:32:06 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.868397 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): -11.30900 36.30000 ymin,ymax (A): -25.82900 22.50000 zmin,zma (A): -10.44400 45.40600 x,y,z range (A): 47.60900 48.32900 55.85000 scale (grids/A): 2.868397 object centre (A): 12.49550 -1.664500 17.48100 number of atom coordinates read : 2769 total number of charged atoms : 2616 net assigned charge : 2.140015 assigned positive charge : 417.9576 centred at (gu) : 90.61664 92.08196 99.23965 assigned negative charge : -415.8183 centred at (gu) : 89.54095 91.48294 98.92046 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23210 grid for indexing accessible points = 1.400000 m= 93975 mr = 135202 m= 34003 mr = 77345 m= 8096 mr = 27563 m= 1144 mr = 6081 m= 98 mr = 791 m= 0 mr = 46 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 5470 time to turn everything in is 1.010000 number of dielectric boundary points 74076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 20925 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) : 1.912265 object centre at (A) : 12.49550 -1.664500 17.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7002409 0.3850427 midg,1,midg; midg,igrid,midg -0.1477667 0.1480785 1,midg,midg; igrid,midg,midg -9.1696382E-02 0.4711268 gauss-seidel spectral radius is 0.9992623 estimated iterations to convergence 291 setup time was (sec) 1.230000 now iterating at: 04:32:08 rms-change max change #iterations 10.37249 365.5557 at 10iterations 6.064225 150.4896 at 20iterations 3.531007 76.12944 at 30iterations 2.060055 44.09502 at 40iterations 1.193517 23.98004 at 50iterations 0.6904622 13.43411 at 60iterations 0.4013734 7.657128 at 70iterations 0.2312042 4.479863 at 80iterations 0.1336004 2.420630 at 90iterations 7.7279940E-02 1.674765 at 100iterations 4.4649910E-02 0.8761978 at 110iterations 2.5801640E-02 0.5157700 at 120iterations 1.4888712E-02 0.2838154 at 130iterations 8.6233309E-03 0.1638107 at 140iterations 4.9920008E-03 8.6282730E-02 at 150iterations 2.9091600E-03 5.0061226E-02 at 160iterations 1.7102152E-03 3.0830383E-02 at 170iterations 1.0183839E-03 2.0292282E-02 at 180iterations finished qdiffx linear iterations at : 04:32:19 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 1.0183839E-03 2.0292282E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 04:32:19 12.619u 0.226s 0:13.17 97.4% 0+0k 0+0io 0pf+0w