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-requ...@gromacs.org.
