Sat Oct 8 23:19:36 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 Sat Oct 8 2011 at 23:19:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6550258 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): 83.68300 125.1770 ymin,ymax (A): 68.40400 120.4650 zmin,zma (A): 54.09800 108.4470 x,y,z range (A): 41.49400 52.06100 54.34900 scale (grids/A): 0.6550258 object centre (A): 104.4300 94.43449 81.27250 number of atom coordinates read : 2260 total number of charged atoms : 2126 net assigned charge : 10.50003 assigned positive charge : 328.1046 centred at (gu) : 91.47967 88.46301 89.34335 assigned negative charge : -317.6053 centred at (gu) : 91.38684 88.43160 89.34937 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6719 nv = 96 ne = 84 npr = 44827 no. pairs analyzed = 44827 no. exposed pairs = 2902 no. arc points = 20600 no. surface atoms = 982 nbur = 1278 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 3596 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3100000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1984 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7309236E-08 1.9454131E-08 midg,1,midg; midg,igrid,midg 2.5301306E-08 2.0148518E-08 1,midg,midg; igrid,midg,midg 7.4322473E-09 4.9072664E-08 gauss-seidel spectral radius is 0.9878978 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 23:19:37 rms-change max change #iterations 0.1438094 20.57504 at 10iterations 1.4856518E-02 2.265701 at 20iterations 1.6133890E-03 0.2340889 at 30iterations 2.1280863E-04 2.9287338E-02 at 40iterations 4.2075513E-05 5.9480667E-03 at 50iterations finished qdiffx linear iterations at : 23:19:39 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 4.2075513E-05 5.9480667E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 23:19:40 3.100u 0.167s 0:03.55 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 Sat Oct 8 2011 at 23:19:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2260 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: 1.965078 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): 83.68300 125.1770 ymin,ymax (A): 68.40400 120.4650 zmin,zma (A): 54.09800 108.4470 x,y,z range (A): 41.49400 52.06100 54.34900 scale (grids/A): 1.965078 object centre (A): 104.4300 94.43449 81.27250 number of atom coordinates read : 2260 total number of charged atoms : 2126 net assigned charge : 10.50003 assigned positive charge : 328.1046 centred at (gu) : 94.43871 85.38889 88.02965 assigned negative charge : -317.6053 centred at (gu) : 94.16086 85.29493 88.04817 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20600 grid for indexing accessible points = 1.400000 m= 26896 mr = 48960 m= 4640 mr = 19753 m= 336 mr = 2964 m= 3 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 990 time to turn everything in is 0.5300000 number of dielectric boundary points 31767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 16819 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) : 0.6550258 object centre at (A) : 104.4300 94.43449 81.27250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6688152E-02 3.8536754E-02 midg,1,midg; midg,igrid,midg 1.6466346E-02 4.1330926E-02 1,midg,midg; igrid,midg,midg -3.2887218E-04 3.5415810E-02 gauss-seidel spectral radius is 0.9986847 estimated iterations to convergence 218 setup time was (sec) 0.7800000 now iterating at: 23:19:41 rms-change max change #iterations 4.028893 190.2944 at 10iterations 1.918316 70.81033 at 20iterations 0.9053370 30.03458 at 30iterations 0.4289572 13.76752 at 40iterations 0.2041207 6.345432 at 50iterations 9.6749924E-02 3.152626 at 60iterations 4.5924608E-02 1.398254 at 70iterations 2.1800820E-02 0.6839390 at 80iterations 1.0389949E-02 0.3218193 at 90iterations 4.9473247E-03 0.1840744 at 100iterations 2.3632960E-03 7.9452515E-02 at 110iterations 1.1295099E-03 3.5940170E-02 at 120iterations finished qdiffx linear iterations at : 23:19:47 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 1.1295099E-03 3.5940170E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 23:19:47 6.882u 0.161s 0:07.39 95.2% 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 Sat Oct 8 2011 at 23:19:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.947616 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): 83.68300 125.1770 ymin,ymax (A): 68.40400 120.4650 zmin,zma (A): 54.09800 108.4470 x,y,z range (A): 41.49400 52.06100 54.34900 scale (grids/A): 2.947616 object centre (A): 104.4300 94.43449 81.27250 number of atom coordinates read : 2260 total number of charged atoms : 2126 net assigned charge : 10.50003 assigned positive charge : 328.1046 centred at (gu) : 96.65815 83.08318 87.04461 assigned negative charge : -317.6053 centred at (gu) : 96.24133 82.94232 87.07219 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 165519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20600 grid for indexing accessible points = 1.400000 m= 85008 mr = 118581 m= 32432 mr = 69127 m= 8473 mr = 26092 m= 1547 mr = 6489 m= 122 mr = 1084 m= 4 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 3299 time to turn everything in is 1.260000 number of dielectric boundary points 71666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 17008 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) : 1.965078 object centre at (A) : 104.4300 94.43449 81.27250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4903067 0.3951949 midg,1,midg; midg,igrid,midg 0.1900223 0.5388315 1,midg,midg; igrid,midg,midg 8.8577373E-03 0.3155287 gauss-seidel spectral radius is 0.9992744 estimated iterations to convergence 293 setup time was (sec) 1.540000 now iterating at: 23:19:49 rms-change max change #iterations 9.502007 327.7099 at 10iterations 5.610074 158.2321 at 20iterations 3.304404 80.40554 at 30iterations 1.935497 47.00789 at 40iterations 1.131241 28.79782 at 50iterations 0.6582246 14.05491 at 60iterations 0.3832006 6.921914 at 70iterations 0.2230105 4.088499 at 80iterations 0.1293780 2.762875 at 90iterations 7.5218603E-02 1.504976 at 100iterations 4.3526798E-02 0.8104956 at 110iterations 2.5242053E-02 0.5286980 at 120iterations 1.4633661E-02 0.3016500 at 130iterations 8.4960414E-03 0.1617435 at 140iterations 4.9274196E-03 9.4894409E-02 at 150iterations 2.8698524E-03 5.7420731E-02 at 160iterations 1.6778589E-03 3.1944275E-02 at 170iterations 9.9500013E-04 2.0805359E-02 at 180iterations finished qdiffx linear iterations at : 23:19:58 total time elapsed so far: 10.89000 # loops : 180 mean,max change (kT/e) : 9.9500013E-04 2.0805359E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 23:19:59 11.066u 0.162s 0:11.50 97.5% 0+0k 0+0io 0pf+0w