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

Ambarnil Ghosh ambargromacs at gmail.com
Mon May 25 18:44:06 CEST 2015

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:

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

Thanks much.

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