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

[Justin Lemkul]

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 
here.

-Justin

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

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