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

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Sat Sep 7 16:03:50 CEST 2019

You need to follow the procedure given in protein ligand system...Somehow
gromacs can't find the .itp file of the ligand which you added in your
topology file.

On Sat 7 Sep, 2019, 6:24 PM Navneet Kumar Singh, <navneetcdl at gmail.com>

> 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
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