[gmx-users] pdb2gmx(ver3.3) contain bug?

[Tomoshi Kameda]

Hi


I'm going to simulate a HEME-Protein complex using GROMACS 3.3, and try

pdb2gmx -f pdb1a6n.ent

and select 
 0: GROMOS96 43a1 force field


But, pdb2gmx cannot link FE(HEME) to NE2(HIS).
pdb2gmx outputs

>Opening library file /home/kameda/gromacs-3.3/share/top/specbond.dat
>5 out of 5 lines of specbond.dat converted succesfully
>Special Atom Distance matrix:
>                 HEME152 HEME152
>                  FE1204 CAB1226
> HEME152 CAB1226   0.565
> HEME152 CAC1234   0.569   0.800

?????

On trial, I type same command using version3.2.1, then output is

> Opening library file /usr/local/share/gromacs/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> Special Atom Distance matrix:
>                    HIS12   HIS24   HIS36   HIS48   HIS64   HIS64   HIS81
>                   NE2109  NE2199  NE2311  NE2430  NE2577  NE2578  NE2697
>    HIS24  NE2199   1.250
>    HIS36  NE2311   2.726   1.886
>    HIS48  NE2430   3.627   2.393   2.106
>    HIS64  NE2577   2.764   1.756   1.685   1.412
>    HIS64  NE2578   2.698   1.666   1.546   1.376   0.151
>    HIS81  NE2697   2.219   2.576   3.044   4.059   2.682   2.694
>    HIS82  NE2707   2.294   2.194   2.241   3.274   1.902   1.905   0.931
>    HIS93  NE2797   2.824   2.010   1.628   1.927   0.622   0.653   2.312
>    HIS97  NE2833   3.213   2.349   1.977   1.830   0.689   0.789   2.620
>   HIS113  NE2973   2.044   1.304   1.082   2.451   2.139   1.994   3.153
>   HIS116 NE21007   1.571   1.352   1.669   3.117   2.612   2.481   2.958
>   HIS116 NE21008   1.389   1.285   1.790   3.192   2.630   2.505   2.849
>   HIS119 NE21044   1.015   0.267   1.997   2.650   1.994   1.904   2.543
>  HEME152  FE1337   2.722   1.843   1.539   1.764   0.440   0.449   2.388
>  HEME152 CAB1359   2.255   1.512   1.325   2.115   0.865   0.806   2.024
>  HEME152 CAC1367   2.930   1.969   1.108   1.581   0.740   0.656   2.769
>                    HIS82   HIS93   HIS97  HIS113  HIS116  HIS116  HIS119
>                   NE2707  NE2797  NE2833  NE2973 NE21007 NE21008 NE21044
>    HIS93  NE2797   1.448
>    HIS97  NE2833   1.794   0.468
>   HIS113  NE2973   2.576   2.261   2.646
>   HIS116 NE21007   2.583   2.666   3.095   0.748
>   HIS116 NE21008   2.524   2.681   3.113   0.893   0.190
>   HIS119 NE21044   2.235   2.203   2.564   1.318   1.217   1.121
>  HEME152  FE1337   1.545   0.214   0.555   2.115   2.541   2.558   2.048
>  HEME152 CAB1359   1.199   0.626   1.082   1.760   2.076   2.078   1.668
>  HEME152 CAC1367   1.878   0.650   0.887   1.881   2.421   2.480   2.169
>                  HEME152 HEME152
>                   FE1337 CAB1359
>  HEME152 CAB1359   0.565
>  HEME152 CAC1367   0.569   0.800
> Linking HIS-93 NE2-797 and HEME-152 FE-1337...

and .top file shows the linkage, for example,

> [atoms]
>  926         NR     93   HIS1    NE2    388      -0.58    14.0067   ; qtot 1
>  1521        FE    152   HEME     FE    643        0.4     55.847   ; qtot 2.4
>.......
> [bonds]
>.......
>  926  1521     2


The line '926  1521     2' does not exist in .top file made by GROMACS
3.3.

For your information, there are not difference between
/home/kameda/gromacs-3.3/share/top/specbond.dat
with
/usr/local/share/gromacs/top/specbond.dat.



Is it caused by Bug ??


Thanks

Tomoshi Kameda