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

Hi Nil, The .gro file does not contain chain information. You can use the .tpr file, or convert the .tpr file to PDB format and use that in stead of the .gro file. Cheers, Tsjerk On Tue, May 26, 2015 at 5:38 AM, Ambarnil Ghosh ambargrom...@gmail.com wrote: Hi Mark and GROMACS users, Thanks

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

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,

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

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 ambargrom...@gmail.com wrote: Dear GROMACS users and experts, My protein is a trimer (ABC) and I am running md : on

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

Hi Mark and GROMACS users, Thanks for your reply. I checked with less but there is no chain information. The file I am loading in VMD: is first *.gro and then loading *.xtc or *.trr files on it. But after loading .gro or .xtc or .trr file ; when I go to the ExtensionsAnalysisSequence