[gmx-users] query regarding missing residues

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 12 18:13:15 CEST 2010

sonali dhindwal wrote:
> Hello Sir,
> I want to ask a question about missing residues, for which coordinates 
> are not defined in the PDB file.
> I have this protein structure and in one of the loop there are some 
> residues whose coordinates are not defined in the file.
> When I did pdb2gmx for preparing the topology, it joined the end of this 
> loop and renumber ed the whole chain there after.
> I searched on net and it was written that missing residues should be 
> modelled somehow before running simulation, but in my case i cant model 
> this loop having missing residues because these are very flexible and i 
> cant define their coordinates through modeling,

"Can't" or "haven't tried"?  Loop reconstruction, though not trivial, is 
routinely applied in such cases.  That's one of the reasons why programs like 
Loopy, Modeller, SwissPDBViewer, etc exist.

> So, if there is someway through which these residues remain missing and 
> still I can go ahead with simulation ?

You're fusing non-consecutive residues.  I would suspect that doing so would 
have negative implications for your results.


> Thanks in advance.
> Regards
> --
> Sonali Dhindwal


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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