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

[Tomoshi Kameda]

> Tomoshi Kameda wrote:
> > 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 ??
> > 
> Not impossible. Please submit a bugzilla and upload the pdb file that 
> works in 3.2.1 and not in 3.3

Thanks David,
I submitted it to bugzilla.

By the way, where do I submit bug for manual?
I already find bug in manual-3.3.pdf......


*********************************************

Tomoshi Kameda, Ph.D.

Computational Biology Research Center(CBRC),
Natinal Institute of Advanced Industrial Science and Technology(AIST)

AIST Tokyo Waterfront Bio-IT research Building,
2-42 Aomi, Koto, Tokyo, Japan 135-0064