[gmx-users] query regarding missing residues

sonali dhindwal sonali11dhindwal at yahoo.co.in
Tue Oct 12 16:44:37 CEST 2010

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

Sonali Dhindwal

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101012/c34c9bcd/attachment.html>

More information about the gromacs.org_gmx-users mailing list