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

[Mark Abraham]

Hi,

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.

Mark

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

> 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 run,
> 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 all
> the chain identifiers are converted to X. That means A,B,C and D - all four
> 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 converted
> 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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