Sun Oct 9 08:09:37 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 Sun Oct 9 2011 at 08:09:37 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2253 !!! WARNING: NAP 276 has a net charge of -2.0000 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: 0.6609729 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): 28.67800 82.53800 ymin,ymax (A): 77.71000 128.8460 zmin,zma (A): 27.86000 74.82000 x,y,z range (A): 53.86000 51.13599 46.96000 scale (grids/A): 0.6609729 object centre (A): 55.60800 103.2780 51.34000 number of atom coordinates read : 2253 total number of charged atoms : 2120 net assigned charge : 3.500021 assigned positive charge : 335.8369 centred at (gu) : 88.55867 92.11903 88.68372 assigned negative charge : -332.3372 centred at (gu) : 88.53732 92.11106 88.73611 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6751 nv = 96 ne = 84 npr = 45939 no. pairs analyzed = 45939 no. exposed pairs = 2747 no. arc points = 19374 no. surface atoms = 926 nbur = 1327 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 3807 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1849 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3550944E-08 1.8033465E-11 midg,1,midg; midg,igrid,midg 5.0063131E-09 1.5911850E-08 1,midg,midg; igrid,midg,midg 6.9575337E-09 9.4323456E-09 gauss-seidel spectral radius is 0.9881091 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 08:09:38 rms-change max change #iterations 0.1612183 28.28432 at 10iterations 1.7088629E-02 2.636665 at 20iterations 1.8478690E-03 0.2978201 at 30iterations 1.9426116E-04 2.9281616E-02 at 40iterations 2.0958452E-05 2.7446747E-03 at 50iterations finished qdiffx linear iterations at : 08:09:41 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.0958452E-05 2.7446747E-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 08:09:41 3.354u 0.174s 0:03.80 92.6% 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 Sun Oct 9 2011 at 08:09:41 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2253 !!! WARNING: NAP 276 has a net charge of -2.0000 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: 1.982919 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): 28.67800 82.53800 ymin,ymax (A): 77.71000 128.8460 zmin,zma (A): 27.86000 74.82000 x,y,z range (A): 53.86000 51.13599 46.96000 scale (grids/A): 1.982919 object centre (A): 55.60800 103.2780 51.34000 number of atom coordinates read : 2253 total number of charged atoms : 2120 net assigned charge : 3.500021 assigned positive charge : 335.8369 centred at (gu) : 85.67609 96.35689 86.05112 assigned negative charge : -332.3372 centred at (gu) : 85.61201 96.33344 86.20834 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19374 grid for indexing accessible points = 1.400000 m= 26534 mr = 51554 m= 4429 mr = 19845 m= 343 mr = 2797 m= 7 mr = 152 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2340 time to turn everything in is 0.3600000 number of dielectric boundary points 30271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 16748 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) : 0.6609729 object centre at (A) : 55.60800 103.2780 51.34000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0017002E-02 1.2127971E-03 midg,1,midg; midg,igrid,midg 8.3354972E-03 4.5081929E-04 1,midg,midg; igrid,midg,midg 9.8686526E-03 1.8789956E-02 gauss-seidel spectral radius is 0.9987036 estimated iterations to convergence 220 setup time was (sec) 0.5800000 now iterating at: 08:09:42 rms-change max change #iterations 4.263865 198.4687 at 10iterations 2.026912 71.28609 at 20iterations 0.9705397 32.96447 at 30iterations 0.4622478 13.85230 at 40iterations 0.2207589 6.768454 at 50iterations 0.1054060 3.290244 at 60iterations 5.0398558E-02 1.652985 at 70iterations 2.4094954E-02 0.7252979 at 80iterations 1.1484099E-02 0.3975685 at 90iterations 5.4896967E-03 0.1959295 at 100iterations 2.6322429E-03 8.7353706E-02 at 110iterations 1.2556391E-03 3.7655711E-02 at 120iterations finished qdiffx linear iterations at : 08:09:49 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.2556391E-03 3.7655711E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 08:09:49 7.742u 0.188s 0:08.21 96.4% 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 Sun Oct 9 2011 at 08:09:49 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2253 !!! WARNING: NAP 276 has a net charge of -2.0000 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: 2.974378 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): 28.67800 82.53800 ymin,ymax (A): 77.71000 128.8460 zmin,zma (A): 27.86000 74.82000 x,y,z range (A): 53.86000 51.13599 46.96000 scale (grids/A): 2.974378 object centre (A): 55.60800 103.2780 51.34000 number of atom coordinates read : 2253 total number of charged atoms : 2120 net assigned charge : 3.500021 assigned positive charge : 335.8369 centred at (gu) : 83.51410 99.53543 84.07664 assigned negative charge : -332.3372 centred at (gu) : 83.41801 99.50021 84.31264 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 169533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19374 grid for indexing accessible points = 1.400000 m= 85236 mr = 124518 m= 31842 mr = 70257 m= 8142 mr = 26048 m= 1375 mr = 6179 m= 144 mr = 947 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 7927 time to turn everything in is 0.9300000 number of dielectric boundary points 68257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 16960 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) : 1.982919 object centre at (A) : 55.60800 103.2780 51.34000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3417945E-02 1.8385254E-02 midg,1,midg; midg,igrid,midg 7.3955387E-02 -0.1607254 1,midg,midg; igrid,midg,midg -3.2283802E-02 0.2883882 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.160000 now iterating at: 08:09:51 rms-change max change #iterations 9.848225 341.4865 at 10iterations 5.776003 144.7320 at 20iterations 3.385688 81.03075 at 30iterations 1.969695 37.78260 at 40iterations 1.144204 27.58603 at 50iterations 0.6636544 12.83961 at 60iterations 0.3851745 6.855064 at 70iterations 0.2220158 4.026634 at 80iterations 0.1284906 2.375862 at 90iterations 7.4169241E-02 1.397856 at 100iterations 4.2831849E-02 0.7727652 at 110iterations 2.4710478E-02 0.4467621 at 120iterations 1.4271108E-02 0.2499313 at 130iterations 8.2295863E-03 0.1467104 at 140iterations 4.7493642E-03 8.3087921E-02 at 150iterations 2.7416088E-03 4.9804688E-02 at 160iterations 1.5771437E-03 2.7511597E-02 at 170iterations 9.0930198E-04 1.5999794E-02 at 180iterations finished qdiffx linear iterations at : 08:10:02 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 9.0930198E-04 1.5999794E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 08:10:02 12.549u 0.214s 0:13.11 97.2% 0+0k 0+0io 0pf+0w