Tue Oct 11 07:07:58 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 Tue Oct 11 2011 at 07:07:58 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3021 !!! WARNING: UMP 491 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5664280 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): -59.49400 3.356000 ymin,ymax (A): -15.78100 41.82200 zmin,zma (A): 5.303000 53.94300 x,y,z range (A): 62.85000 57.60300 48.64000 scale (grids/A): 0.5664280 object centre (A): -28.06900 13.02050 29.62300 number of atom coordinates read : 3021 total number of charged atoms : 2878 net assigned charge : -3.099987 assigned positive charge : 442.2254 centred at (gu) : 88.44076 89.46847 90.53929 assigned negative charge : -445.3260 centred at (gu) : 88.64967 89.57943 90.56223 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6319 nv = 96 ne = 84 npr = 62690 no. pairs analyzed = 62690 no. exposed pairs = 3766 no. arc points = 26884 no. surface atoms = 1279 nbur = 1742 mkacc time = 0.1400000 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 = 1.512000 m= 266 mr = 3300 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2680 ## 310 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8107 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3620316E-10 -8.9787550E-10 midg,1,midg; midg,igrid,midg 1.1981335E-09 -1.7879892E-09 1,midg,midg; igrid,midg,midg 3.4693008E-09 -2.3695894E-09 gauss-seidel spectral radius is 0.9839245 estimated iterations to convergence 65 setup time was (sec) 0.5700000 now iterating at: 07:07:59 rms-change max change #iterations 8.8703550E-02 17.17283 at 10iterations 6.4302599E-03 1.015379 at 20iterations 5.1455683E-04 7.9204559E-02 at 30iterations 5.3499833E-05 1.3280869E-02 at 40iterations 8.7317994E-06 2.1533966E-03 at 50iterations finished qdiffx linear iterations at : 07:08:02 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 8.7317994E-06 2.1533966E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 07:08:02 3.427u 0.206s 0:03.95 91.6% 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 Tue Oct 11 2011 at 07:08:02 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3021 !!! WARNING: UMP 491 has a net charge of -0.1000 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: 1.699284 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): -59.49400 3.356000 ymin,ymax (A): -15.78100 41.82200 zmin,zma (A): 5.303000 53.94300 x,y,z range (A): 62.85000 57.60300 48.64000 scale (grids/A): 1.699284 object centre (A): -28.06900 13.02050 29.62300 number of atom coordinates read : 3021 total number of charged atoms : 2878 net assigned charge : -3.099987 assigned positive charge : 442.2254 centred at (gu) : 85.32179 88.40461 91.61726 assigned negative charge : -445.3260 centred at (gu) : 85.94877 88.73793 91.68624 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69783 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26884 grid for indexing accessible points = 1.400000 m= 22393 mr = 47386 m= 2425 mr = 15818 m= 87 mr = 1263 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 852 time to turn everything in is 0.5000000 number of dielectric boundary points 30207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 22249 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) : 0.5664280 object centre at (A) : -28.06900 13.02050 29.62300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6476067E-03 1.2187229E-02 midg,1,midg; midg,igrid,midg 2.8720596E-03 -3.0239664E-02 1,midg,midg; igrid,midg,midg -1.0521833E-03 -2.5591748E-02 gauss-seidel spectral radius is 0.9983355 estimated iterations to convergence 195 setup time was (sec) 0.8000000 now iterating at: 07:08:03 rms-change max change #iterations 3.618724 196.3818 at 10iterations 1.558145 55.76912 at 20iterations 0.6737897 25.50634 at 30iterations 0.2912090 11.10616 at 40iterations 0.1257761 4.254320 at 50iterations 5.4529797E-02 2.019650 at 60iterations 2.3622062E-02 0.7976837 at 70iterations 1.0204568E-02 0.3678789 at 80iterations 4.4328286E-03 0.1488419 at 90iterations 1.9299653E-03 7.2595596E-02 at 100iterations 8.4110565E-04 2.9741287E-02 at 110iterations 3.6786235E-04 1.1692047E-02 at 120iterations finished qdiffx linear iterations at : 07:08:10 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 3.6786235E-04 1.1692047E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 07:08:10 7.634u 0.236s 0:08.23 95.5% 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 07:08:10 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3021 !!! WARNING: UMP 491 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.548926 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): -59.49400 3.356000 ymin,ymax (A): -15.78100 41.82200 zmin,zma (A): 5.303000 53.94300 x,y,z range (A): 62.85000 57.60300 48.64000 scale (grids/A): 2.548926 object centre (A): -28.06900 13.02050 29.62300 number of atom coordinates read : 3021 total number of charged atoms : 2878 net assigned charge : -3.099987 assigned positive charge : 442.2254 centred at (gu) : 82.98255 87.60672 92.42569 assigned negative charge : -445.3260 centred at (gu) : 83.92301 88.10662 92.52930 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 161651 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26884 grid for indexing accessible points = 1.400000 m= 76213 mr = 115404 m= 23193 mr = 61015 m= 3851 mr = 17841 m= 308 mr = 2581 m= 9 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2843 time to turn everything in is 1.170000 number of dielectric boundary points 68204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 23009 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) : 1.699284 object centre at (A) : -28.06900 13.02050 29.62300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1231808 0.1910833 midg,1,midg; midg,igrid,midg 8.8449568E-02 -0.5265969 1,midg,midg; igrid,midg,midg -9.1041707E-02 -0.4643844 gauss-seidel spectral radius is 0.9991882 estimated iterations to convergence 277 setup time was (sec) 1.490000 now iterating at: 07:08:12 rms-change max change #iterations 9.115138 282.2843 at 10iterations 5.191165 106.0625 at 20iterations 2.955527 63.32237 at 30iterations 1.663988 40.68570 at 40iterations 0.9387649 21.51965 at 50iterations 0.5276157 11.21340 at 60iterations 0.2967747 5.965931 at 70iterations 0.1662603 3.589588 at 80iterations 9.3048394E-02 1.890348 at 90iterations 5.2192602E-02 1.144832 at 100iterations 2.9229131E-02 0.5703926 at 110iterations 1.6337136E-02 0.3603592 at 120iterations 9.1400286E-03 0.1757145 at 130iterations 5.1099476E-03 9.8182678E-02 at 140iterations 2.8564644E-03 5.7441711E-02 at 150iterations 1.5992377E-03 3.1106949E-02 at 160iterations 8.9200021E-04 1.7691761E-02 at 170iterations 5.0031679E-04 9.9181831E-03 at 180iterations finished qdiffx linear iterations at : 07:08:23 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 5.0031679E-04 9.9181831E-03 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 07:08:23 12.292u 0.265s 0:12.85 97.6% 0+0k 0+0io 0pf+0w