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

[Ambarnil Ghosh]

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