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

mary ko maryko2019 at yahoo.com
Mon Feb 25 22:36:38 CET 2019

 Thank you Justin. I am actually following the protein-ligand tutorial to do simulations of my protein-ligand system. I skipped the python cgenff_charmm2gmx.py... Because of the mismatch of cgenff error couldnt be fixed. I have the bgc which is beta-D-glucose and built its .gro file as a ligand and protein-processed.gro and I copied the ligand in the protein-processed.gro to have the complex.gro. I also use charmm36-nov2018 and added it in the force fields with the Bglc to Bgc change in merged.rtp. Now that I try to build the topology.top file with pdb2gmx or even x2top there is an error: atom ot1 in residue Phe was not found in rtp entry Phe with 20 atoms while sorting atoms for pdb2gmx and could only find a force field type for 19078 out of 21750 atoms for x2top. What do you think I should do to build the topology?Thanks.
    On Saturday, February 23, 2019, 6:50:39 PM EST, Justin Lemkul <jalemkul at vt.edu> wrote:  

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
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


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