[gmx-users] Renaming of the chains in time of simulation (like ABC...to X)

Ambarnil Ghosh ambargromacs at gmail.com
Tue May 26 05:38:52 CEST 2015

Hi Mark and GROMACS users,

Thanks for your reply.

I checked with less but there is no chain information.

The file I am loading in VMD:  is first  *.gro   and then loading  *.xtc or
*.trr  files on it. But after loading .gro or .xtc or .trr file ; when I go
to the "Extensions>>Analysis>>Sequence Viewer" of the vmd-GUI, it shows
that all the chain names are X only.

Therefore, I also checked that in the other .gro files which I used in time
of md-preparation are also chainX (like in mymoleculename_processed.gro,
the output of pdb2gmx is chainX only ). Because, I think chain informations
exist only in the topology files (.top and .itp).

So the difficulties I am facing is how to load the information from the
.top and .itp files in vmd. Thus, I can visualize the chain sepreately (all
four chains A,B,C and D) and measure each chain's RMSD change seperately by
saving trajectoories for each chain.

Thanks again for the reply.
Please help.

Thanking you

Date: Mon, 25 May 2015 18:01:11 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Renaming of the chains in time of simulation
        (like ABC...to X)
        <CAMNuMAQtRFh0CR8m8=hCAHLW1aU0axAY_DvNLZqUrJiDd7cpag at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8


Does the file you're opening in VMD have any information about the chain?
You'll need to look at it, e.g. with less.


On Mon, May 25, 2015 at 6:44 PM Ambarnil Ghosh <ambargromacs at gmail.com>

> Dear GROMACS users and experts,
> My protein is a trimer (ABC) and I am running md :  on binding of a small
> peptide (chain-D) to a trimer (chain ABC). The peptide binds with both A
> and B (that means near interface region)
> I am following the lysozyme tutorial to build the run. I completed the
> but when I was trying to analyze the rmsd-graph of the D-peptide only
> (ligand peptide), it is becoming difficult to separate the chains.
> Because in the vmd, when I am opening the trajectory file, I found that
> the chain identifiers are converted to X. That means A,B,C and D - all
> chains are renamed as X.
> In the topology files, i checked that all the chains and their name are
> proper and separate, like in files:
> topol_Protein_chain_A.itp
> topol_Protein_chain_B.itp
> topol_Protein_chain_C.itp
> topol_Protein_chain_D.itp
> Therefore, my question is: when the chain-identifiers are getting
> to X? And how can I correct this? May be I am missing some very basic
> thing, but I can't find which one.
> I am new to multimeric simulation, any kind of help/lead is much
> appreciated!
> Thanks much.
> Sincerely
> Nil

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