[gmx-users] residue IDs are not ordered in gro file.

[Justin A. Lemkul]

BIN ZHANG wrote:
> Hi, there:
> 
> I found that in gromacs version 4.5.1, the residue ids are not ordered 
> consecutively as before in the .gro file. For example, if I have two 
> chains in the protein, then the residue ids will be ordered with respect 
> to each individual chain, rather than reordered to be a complete system. 
> I also attached one segment in the gro file for illustration.
> 
> Is this supposed to be a new feature? It's actually quite inconvenient 
> when trying to make selection in VMD.
> 

The default behavior is now to not renumber the residues in the original 
coordinate file passed to pdb2gmx.  I suspect that there were missing residues 
at the N-terminus of your second chain, at least.  To disable the feature, use 
pdb2gmx -renum.

-Justin

> Thanks,
> Bin
> 
> 
> ==========================
>   816VAL   HG1313296   3.455   7.611  11.465  0.7230 -0.9675 -4.0812
>   816VAL    CG213297   3.630   7.461  11.621 -0.5958  0.7701  0.1938
>   816VAL   HG2113298   3.680   7.555  11.591  0.2600  0.8421  1.7585
>   816VAL   HG2213299   3.571   7.503  11.705  2.5960  0.5799  2.7250
>   816VAL   HG2313300   3.714   7.394  11.646 -0.5850  1.1199  1.1233
>   816VAL      C13301   3.390   7.261  11.629 -0.6898  0.0472 -0.1581
>   816VAL    OT113302   3.270   7.268  11.592 -0.7354 -0.1123 -0.0378
>   816VAL    OT213303   3.418   7.233  11.749  0.0205  0.1649 -0.2904
>     8ALA      N13304   4.101   8.322   6.962  0.4051 -0.3543 -0.0582
>     8ALA     H113305   4.012   8.374   6.969  1.1832  1.0474 -0.2561
>     8ALA     H213306   4.179   8.374   7.007 -0.8226  0.0271  1.7227
>     8ALA     H313307   4.089   8.236   7.020 -2.0801 -1.0654 -1.4588
>     8ALA     CA13308   4.132   8.290   6.820  0.4700  0.4977 -0.2390
>     8ALA     HA13309   4.051   8.228   6.785 -1.3315  1.9366  1.1423
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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