[gmx-users] RMSD comparison to a different reference structure.

[Natalie Stephenson]

Perfect! Hadn't thought of that! 

Was hoping to look at side chain fluctuations as well, but I think if I have the c-alpha comparison to WT and then side chain comparison to self, that should work well. 

Thanks for your help!!! 

Natalie


________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Erik Marklund [erik.marklund at chem.ox.ac.uk]
Sent: 07 September 2015 11:42
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] RMSD comparison to a different reference structure.

Hi,

How about comparing only C-alphas? As long as you have the same number of residues, that should work. You need to make reduced versions of your tpr and trajectory files.

Kind regards,
Erik


Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

> On 7 Sep 2015, at 09:32, Natalie Stephenson <natalie.stephenson at manchester.ac.uk> wrote:
>
>
>
> Hi,
>
> I was wondering if you would be able to advise me of the best method to compare a mutated and WT structure. I was hoping to perform RMSD analysis for certain regions within a mutation against the same region within the wild type structure. Unfortunately, the atom numbering is likely to be off for some regions, as the mutation with add/remove atoms. As only one index file is specified for the g_rms command I wondered how best to do this? Or if it was possible?
>
> Thanks,
> Natalie
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