[gmx-users] query regarding missing residues

[sonali dhindwal]

Hello Justin and Mark,

Thanks for the reply.
Reason that I didnt apply loop modelling was, for that region it is not given in literature that, this region which consist of 10 residues will form a helix of will remain in loop in an disorganized way. Therefore, I was reluctant in doing loop reconstruction without prior information of this building as loop or helix.

And u rightly said that fusing non-corresponding residues will give wrong results, that's why I was asking that if there is way to go for simulation while having some missing residues.
But your replies suggest that the answer is no.

So, I will go for loop reconstruction and will then see what happens.

Regards


Thanks and Regards 

--
Sonali Dhindwal

--- On Tue, 12/10/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] query regarding missing residues
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Tuesday, 12 October, 2010, 9:43 PM



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.

-Justin

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

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

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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