[gmx-users] Residue BGC not found in the database

Justin Lemkul jalemkul at vt.edu
Sun Feb 24 00:50:18 CET 2019

On 2/20/19 11:19 AM, mary ko wrote:
> Dear all,
> I face the 'Residue BGC not found in the database' error when I try to build the topology file of my protein-ligand system by pdb2gmx -f pro.pdb. I used Charmm force field but I tried it with all the other force fields as well to see if the problem could be solved which was useless. I searched the list and errors-gromacs in the website and found that the simplest way is to change the name of this residue. As I am not familiar with protein structure, I do not know what changes may be helpful to pass this error. also, it is said that one way is to parameterize the residue which I do not know how to do that. Your help would be highly appreciated.Thanks!

If "BGC" is a synonym for beta-D-glucose, that is called BGLC in CHARMM, 
so you just need to rename the residue accordingly. If it is some other 
unknown species, then yes, you need to parametrize it yourself.



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