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

Mark Abraham mark.j.abraham at gmail.com
Mon May 25 20:01:13 CEST 2015


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 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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list