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

Navneet Kumar Singh navneetcdl at gmail.com
Sat Sep 7 14:53:35 CEST 2019

Hello Everyone!

I am trying to simulate 5 peptides, 10 small molecules (UNK) and water.
I have used PACKMOL to make system having all these 3 ingredients.
Peptides terminal residues were capped using ACE and NME in the pymol.
It is pretty much straight forward simulating peptides with water as all
necessary parameters are already defined.
But When I am having UNK (A SMALL MOLECULE) in my system, its throwing
error i.e. (Residue 'UNK' not found in residue topology database) and this
is pretty much obvious that pdb2gmx can't find any UNK.

During protein-ligand simulations we first get the .gro files for protein
using pdb2gmx, similarly we prepare topology files for small molecules
according to force field on some server or acpype. and then we combine the
.gro files of protein and ligand, simultaneously update the topology files.
then process continuous as usual.

Here I have a .pdb file containing peptides and small molecules along with
water prepared using the PACKMOL.
How to deal with ligand. I have processed the one ligand according CHARMM
force field (using CHARMM36 ) from CGenFF <https://cgenff.umaryland.edu/>.
I have all .itp, .prm and other files. But how to add and proceed furthur?

     Thanks & Regards

[image: photo]

Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)

E navneetcdl at gmail.com  <navneetcdl at gmail.com>

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