<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hello Justin and Mark,<br><br>Thanks for the reply.<br>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.<br><br>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.<br>But your replies suggest that the answer is no.<br><br>So, I will go for loop reconstruction and will then see what happens.<br><br>Regards<br><br><br>Thanks and Regards <br><br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Tue, 12/10/10, Justin A. Lemkul <i><jalemkul@vt.edu></i></b>
wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] query regarding missing residues<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Tuesday, 12 October, 2010, 9:43 PM<br><br><div class="plainMail"><br><br>sonali dhindwal wrote:<br>> Hello Sir,<br>> <br>> I want to ask a question about missing residues, for which coordinates are not defined in the PDB file.<br>> I have this protein structure and in one of the loop there are some residues whose coordinates are not defined in the file.<br>> When I did pdb2gmx for preparing the topology, it joined the end of this loop and renumber ed the whole chain there after.<br>> 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,<br><br>"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.<br><br>> So, if there is someway through which these residues remain missing and still I can go ahead with simulation ?<br><br>You're fusing non-consecutive residues. I would suspect that doing so would have negative implications for your results.<br><br>-Justin<br><br>> Thanks in advance.<br>> Regards<br>> <br>> --<br>> Sonali Dhindwal<br>> <br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a
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