[gmx-users] Residue 'UNK' not found in residue topology database

[Justin Lemkul]

On 9/12/19 2:02 PM, Navneet Kumar Singh wrote:
> Yes, I succeed in running NVT and NPT without any error. But when I
> visualized the whole complex system (.gro) file in VMD/CHIMERA. It was like
> (Please download .JPG from the below link)
>
> https://fil.email/1pKxlHXy
>
> I have attached a snapshot.
> It looks like something weird problem with co-ordinates, 2 molecules are
> connected with abnormal large bonds. These are the drug/small molecules.
> What problem it can be ?

http://manual.gromacs.org/current/user-guide/terminology.html#periodic-boundary-conditions

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================