Sat Oct 15 14:18:53 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 Sat Oct 15 2011 at 14:18:53 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4807 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5133307 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): -18.28900 37.35700 ymin,ymax (A): -30.85800 35.53000 zmin,zma (A): -4.175000 65.17600 x,y,z range (A): 55.64600 66.38800 69.35101 scale (grids/A): 0.5133307 object centre (A): 9.534001 2.336001 30.50050 number of atom coordinates read : 4807 total number of charged atoms : 4556 net assigned charge : 5.706031 assigned positive charge : 722.4623 centred at (gu) : 90.04316 90.20975 88.44073 assigned negative charge : -716.7610 centred at (gu) : 89.94006 90.25730 88.44907 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8010 nv = 96 ne = 84 npr = 97150 no. pairs analyzed = 97150 no. exposed pairs = 6154 no. arc points = 42408 no. surface atoms = 2063 nbur = 2744 mkacc time = 0.2000000 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 = 1.652000 m= 277 mr = 4102 m= 0 mr = 7 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4121 ## 600 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10666 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7289112E-10 4.5329469E-11 midg,1,midg; midg,igrid,midg 2.1669501E-10 -5.1538562E-11 1,midg,midg; igrid,midg,midg -2.1130092E-10 3.9212558E-10 gauss-seidel spectral radius is 0.9805959 estimated iterations to convergence 59 setup time was (sec) 0.6500000 now iterating at: 14:18:54 rms-change max change #iterations 7.1746692E-02 9.946682 at 10iterations 5.3365743E-03 1.043201 at 20iterations 1.0576017E-03 0.1705933 at 30iterations 3.7623756E-04 4.4920921E-02 at 40iterations 1.5185188E-04 2.0468784E-02 at 50iterations finished qdiffx linear iterations at : 14:18:57 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.5185188E-04 2.0468784E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 14:18:57 3.290u 0.145s 0:03.82 89.7% 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 15 2011 at 14:18:57 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4807 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.539992 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): -18.28900 37.35700 ymin,ymax (A): -30.85800 35.53000 zmin,zma (A): -4.175000 65.17600 x,y,z range (A): 55.64600 66.38800 69.35101 scale (grids/A): 1.539992 object centre (A): 9.534001 2.336001 30.50050 number of atom coordinates read : 4807 total number of charged atoms : 4556 net assigned charge : 5.706031 assigned positive charge : 722.4623 centred at (gu) : 90.12800 90.62767 85.32042 assigned negative charge : -716.7610 centred at (gu) : 89.81995 90.77166 85.34701 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 91089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26387 mr = 62533 m= 2265 mr = 17278 m= 47 mr = 922 m= 1 mr = 4 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 39053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 489 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 34283 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) : 0.5133307 object centre at (A) : 9.534001 2.336001 30.50050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5126182E-03 1.6912315E-02 midg,1,midg; midg,igrid,midg 6.3911332E-03 -1.1593089E-02 1,midg,midg; igrid,midg,midg -6.1745662E-04 1.2206217E-02 gauss-seidel spectral radius is 0.9981416 estimated iterations to convergence 184 setup time was (sec) 0.9000000 now iterating at: 14:18:58 rms-change max change #iterations 3.851272 142.3096 at 10iterations 1.587630 49.98377 at 20iterations 0.6567552 20.56147 at 30iterations 0.2712452 8.379354 at 40iterations 0.1125470 3.637438 at 50iterations 4.6821084E-02 1.565194 at 60iterations 1.9471811E-02 0.6181049 at 70iterations 8.1925187E-03 0.2651367 at 80iterations 3.5496308E-03 0.1132083 at 90iterations 1.6425094E-03 6.0485005E-02 at 100iterations 8.5687340E-04 2.6517868E-02 at 110iterations 5.1975943E-04 1.5369356E-02 at 120iterations finished qdiffx linear iterations at : 14:19:05 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 5.1975943E-04 1.5369356E-02 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 14:19:05 7.225u 0.186s 0:07.72 95.8% 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 15 2011 at 14:19:05 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4807 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.309988 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): -18.28900 37.35700 ymin,ymax (A): -30.85800 35.53000 zmin,zma (A): -4.175000 65.17600 x,y,z range (A): 55.64600 66.38800 69.35101 scale (grids/A): 2.309988 object centre (A): 9.534001 2.336001 30.50050 number of atom coordinates read : 4807 total number of charged atoms : 4556 net assigned charge : 5.706031 assigned positive charge : 722.4623 centred at (gu) : 90.19158 90.94096 82.98042 assigned negative charge : -716.7610 centred at (gu) : 89.73003 91.15744 83.02055 start vw surface at 0.1900000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 212310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95313 mr = 153702 m= 23515 mr = 74217 m= 3253 mr = 16420 m= 196 mr = 1925 m= 1 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 88256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 36364 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) : 1.539992 object centre at (A) : 9.534001 2.336001 30.50050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1764813 0.4589246 midg,1,midg; midg,igrid,midg 6.6940121E-02 -0.2843467 1,midg,midg; igrid,midg,midg -3.7073898E-03 0.1819594 gauss-seidel spectral radius is 0.9991743 estimated iterations to convergence 275 setup time was (sec) 1.770000 now iterating at: 14:19:07 rms-change max change #iterations 10.46791 292.0464 at 10iterations 6.034286 164.9930 at 20iterations 3.466335 79.38657 at 30iterations 1.965265 45.85442 at 40iterations 1.114930 24.84990 at 50iterations 0.6288376 13.56309 at 60iterations 0.3537933 8.134206 at 70iterations 0.1990713 4.176102 at 80iterations 0.1117778 2.101280 at 90iterations 6.2735170E-02 1.452194 at 100iterations 3.5093300E-02 0.7098963 at 110iterations 1.9619642E-02 0.3769255 at 120iterations 1.0977942E-02 0.2210913 at 130iterations 6.1416361E-03 0.1197262 at 140iterations 3.4385384E-03 6.7886353E-02 at 150iterations 1.9327950E-03 3.6214352E-02 at 160iterations 1.0920365E-03 2.0350218E-02 at 170iterations 6.2353472E-04 1.1579514E-02 at 180iterations finished qdiffx linear iterations at : 14:19:17 total time elapsed so far: 11.60000 # loops : 180 mean,max change (kT/e) : 6.2353472E-04 1.1579514E-02 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.77000 DelPhi exited at 14:19:18 11.775u 0.194s 0:12.42 96.2% 0+0k 0+0io 0pf+0w