[gmx-users] Regarding Residue in chain has different type (Other) from starting residue

Justin Lemkul jalemkul at vt.edu
Mon Oct 16 14:03:34 CEST 2017

On 10/15/17 11:27 PM, Dilip H N wrote:
> Thank you Justin Sir,
> 1] But how do i solve this issue..?? and make sure that pdb2gmx is not
> interpreting my input as being a single chain and it's finding dissimilar
> residue types..?? even i tried with gmx pdb2gmx with -ter command, but
> still, i am getting the same results....

There's no indication of a problem. If your input PDB file doesn't have 
TER delimiters between chains, then pdb2gmx -ter will do nothing.

> 2] If i view the structure in VMD and type protein in Graphical
> representations->selected atoms, I am viewing only Glycine, and if i type
> resname TMAO then i am viewing the tmao molecules ..., any inference here
> can i have here..??

No, because what you see in VMD has no bearing on what pdb2gmx 
interprets. But as far as I can see, there's no actual problem to solve 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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