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

[Justin A. Lemkul]

BIN ZHANG wrote:
> 
> Dear Justin:
> 
> Thanks a lot for your reply.
> 
> I indeed have missing residues in the second chain. However, when I try 
> pdb2gmx -renum, it renumbers the second chain starting from 1, rather 
> than starting from 817(Nres_1st+1).
> 

To get consecutive numbering, you may have to merge the chains.  You can do this 
with pdb2gmx -chainsep.

-Justin

> Thanks,
> Bin
> 
> 
> 
> =====================================
>   816VAL   HG1313296  -3.347   0.716   6.099
>   816VAL    CG213297  -3.088   0.611   6.105
>   816VAL   HG2113298  -3.036   0.707   6.088
>   816VAL   HG2213299  -3.131   0.613   6.208
>   816VAL   HG2313300  -3.013   0.530   6.100
>   816VAL      C13301  -3.375   0.483   6.144
>   816VAL    OT113302  -3.466   0.460   6.111
>   816VAL    OT213303  -3.326   0.517   6.224
>     1ALA      N13304  -2.528   1.672   1.358
>     1ALA     H113305  -2.582   1.754   1.340
>     1ALA     H213306  -2.430   1.694   1.354
>     1ALA     H313307  -2.550   1.635   1.448
>     1ALA     CA13308  -2.558   1.573   1.259
> 
>>

-- 
========================================

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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