[gmx-users] query regarding missing residues

Mark Abraham mark.abraham at anu.edu.au
Tue Oct 12 17:33:27 CEST 2010

----- Original Message -----
From: sonali dhindwal <sonali11dhindwal at yahoo.co.in>
Date: Wednesday, October 13, 2010 1:44
Subject: [gmx-users] query regarding missing residues
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

| > 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,

Accordingly, you don't need to be too rigorous in generating something plausible to connect the ragged ends. It will move around plenty during MD. There should be many molecule builders that will allow you to add on a new residue, tweak the dihedrals and so on, eventually filling the gap.

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

You may find some suggestions here : http://www.gromacs.org/Documentation/File_Formats/Coordinate_File


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