[gmx-users] how to keep chain ID?

Justin Lemkul jalemkul at vt.edu
Mon Oct 22 12:19:26 CEST 2012

On 10/22/12 6:14 AM, Albert wrote:
> hello:
> I've got a large protein contains five chains. I assigned the FF with PDB2GMX
> and it split them into different .itp file. after running minimization, I found
> that the em.gro contains no chain informations. I use
> editconf -f em.gro -o em.pdb
> to convert it into .pdb file and it doesn't have chain ID either.
> I am wondering, how can I keep chain ID informations?

Use .pdb format throughout your workflow.  The .gro format has no space for 
chain identifiers so the information is lost.  You may be able to use trjconv 
(instead of editconf) to convert back to .pdb using a .tpr file, which may have 
chain identifier information from the topology (I seem to vaguely recollect this).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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