[gmx-users] trjconv and missing chain identifier

Mark Abraham Mark.Abraham at anu.edu.au
Fri Mar 2 16:23:57 CET 2007

Una Bjarnadottir wrote:
> Dear Users, 
> I'm converting trajectory files into .pdb files and when I there is only
> one chain in them f.eks. only the  prtotein but not ligand or inhibitor
> it does not set any chain identifier to the output .pdb files.  When I
> have ligand and inhibitor in them the output will have chains A-B-C.
> I tryed whatif but it can't read the big overall file.  
> The chain identifier is nessarry in some grafics programs so I really
> need this.
> Hope you can help, it will be hightly appreciated.

gromacs discards chain identifiers from PDB files when it reads them 
with pdb2gmx and will not re-create them.

Probably free software like VMD http://www.ks.uiuc.edu/Research/vmd/ can 
do what you need without these chain problems, rather than the graphics 
program you're planning to use.

I appreciate that English may not be your first language, but please do 
consider proof-reading your posts and/or using a spell-checker before 
you send. People on this list are much more likely to help you if you 
make it easy for them to do so, rather than work at trying to piece 
together your problem.


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