Sat Oct 15 14:18:34 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 14:18:34 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4763 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5134344 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): -18.81700 36.48200 ymin,ymax (A): -30.58000 34.69300 zmin,zma (A): -3.878000 65.45900 x,y,z range (A): 55.29900 65.27300 69.33700 scale (grids/A): 0.5134344 object centre (A): 8.832501 2.056500 30.79050 number of atom coordinates read : 4763 total number of charged atoms : 4513 net assigned charge : 8.106028 assigned positive charge : 716.5926 centred at (gu) : 90.39769 90.52129 88.33659 assigned negative charge : -708.4908 centred at (gu) : 90.28551 90.53865 88.29623 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7815 nv = 96 ne = 84 npr = 97176 no. pairs analyzed = 97176 no. exposed pairs = 6049 no. arc points = 41978 no. surface atoms = 2024 nbur = 2739 mkacc time = 0.1700000 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= 296 mr = 3980 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4036 ## 584 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 10446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7606142E-11 1.6111780E-10 midg,1,midg; midg,igrid,midg 1.5855853E-10 9.2010684E-11 1,midg,midg; igrid,midg,midg -1.7773436E-10 5.0065718E-10 gauss-seidel spectral radius is 0.9805964 estimated iterations to convergence 59 setup time was (sec) 0.5600000 now iterating at: 14:18:35 rms-change max change #iterations 7.0235379E-02 9.788261 at 10iterations 4.5928769E-03 0.7214890 at 20iterations 8.3970529E-04 0.1069050 at 30iterations 3.1206844E-04 4.5819581E-02 at 40iterations 1.2111685E-04 1.9310236E-02 at 50iterations finished qdiffx linear iterations at : 14:18:39 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.2111685E-04 1.9310236E-02 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 14:18:40 4.199u 0.268s 0:05.30 83.9% 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 Sat Oct 15 2011 at 14:18:40 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4763 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.540303 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): -18.81700 36.48200 ymin,ymax (A): -30.58000 34.69300 zmin,zma (A): -3.878000 65.45900 x,y,z range (A): 55.29900 65.27300 69.33700 scale (grids/A): 1.540303 object centre (A): 8.832501 2.056500 30.79050 number of atom coordinates read : 4763 total number of charged atoms : 4513 net assigned charge : 8.106028 assigned positive charge : 716.5926 centred at (gu) : 91.19192 91.56250 85.00842 assigned negative charge : -708.4908 centred at (gu) : 90.85636 91.61570 84.88876 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 88432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41978 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 24930 mr = 60349 m= 2165 mr = 16094 m= 46 mr = 891 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.4600000 number of dielectric boundary points 38239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 555 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 33974 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) : 0.5134344 object centre at (A) : 8.832501 2.056500 30.79050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3350929E-03 2.3199596E-02 midg,1,midg; midg,igrid,midg 3.1321542E-04 -8.5923728E-03 1,midg,midg; igrid,midg,midg -4.4054349E-04 1.3058678E-02 gauss-seidel spectral radius is 0.9981324 estimated iterations to convergence 184 setup time was (sec) 0.7400000 now iterating at: 14:18:41 rms-change max change #iterations 3.842619 155.2947 at 10iterations 1.575268 56.47325 at 20iterations 0.6530774 22.70844 at 30iterations 0.2684995 8.107125 at 40iterations 0.1107248 3.441322 at 50iterations 4.5998961E-02 1.680237 at 60iterations 1.8952956E-02 0.6468048 at 70iterations 7.8977328E-03 0.2512474 at 80iterations 3.3699619E-03 0.1132545 at 90iterations 1.4803729E-03 5.1711082E-02 at 100iterations 7.1257219E-04 2.2491455E-02 at 110iterations 3.9468633E-04 1.3830185E-02 at 120iterations finished qdiffx linear iterations at : 14:18:57 total time elapsed so far: 9.110000 # loops : 120 mean,max change (kT/e) : 3.9468633E-04 1.3830185E-02 energy calculations done at 9.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.250000 DelPhi exited at 14:18:58 9.251u 0.302s 0:18.07 52.8% 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 14:18:58 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4763 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.310455 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): -18.81700 36.48200 ymin,ymax (A): -30.58000 34.69300 zmin,zma (A): -3.878000 65.45900 x,y,z range (A): 55.29900 65.27300 69.33700 scale (grids/A): 2.310455 object centre (A): 8.832501 2.056500 30.79050 number of atom coordinates read : 4763 total number of charged atoms : 4513 net assigned charge : 8.106028 assigned positive charge : 716.5926 centred at (gu) : 91.78760 92.34325 82.51233 assigned negative charge : -708.4908 centred at (gu) : 91.28444 92.42340 82.33321 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 206163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41978 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 89772 mr = 147997 m= 21976 mr = 69488 m= 3114 mr = 15355 m= 199 mr = 1879 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 1.140000 number of dielectric boundary points 86440 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 36012 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) : 1.540303 object centre at (A) : 8.832501 2.056500 30.79050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1325420 0.5397146 midg,1,midg; midg,igrid,midg -0.1061317 -0.2480560 1,midg,midg; igrid,midg,midg 6.7127803E-05 0.2062054 gauss-seidel spectral radius is 0.9991693 estimated iterations to convergence 274 setup time was (sec) 1.440000 now iterating at: 14:19:00 rms-change max change #iterations 10.36574 337.6616 at 10iterations 5.973740 154.3401 at 20iterations 3.408662 80.07636 at 30iterations 1.934639 42.87225 at 40iterations 1.093141 22.39166 at 50iterations 0.6165183 12.49592 at 60iterations 0.3469789 6.922207 at 70iterations 0.1941343 4.202276 at 80iterations 0.1089186 2.149866 at 90iterations 6.0930382E-02 1.255138 at 100iterations 3.4015626E-02 0.6772135 at 110iterations 1.8999869E-02 0.3962383 at 120iterations 1.0595175E-02 0.2120781 at 130iterations 5.9292978E-03 0.1128044 at 140iterations 3.3108492E-03 6.6627502E-02 at 150iterations 1.8548769E-03 3.6735535E-02 at 160iterations 1.0430620E-03 2.4520874E-02 at 170iterations 5.9422053E-04 1.1446714E-02 at 180iterations finished qdiffx linear iterations at : 14:19:14 total time elapsed so far: 15.63000 # loops : 180 mean,max change (kT/e) : 5.9422053E-04 1.1446714E-02 energy calculations done at 15.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.76000 DelPhi exited at 14:19:14 15.760u 0.331s 0:16.37 98.2% 0+0k 0+0io 0pf+0w