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

Justin Lemkul jalemkul at vt.edu
Thu Sep 12 15:25:41 CEST 2019

On 9/7/19 1:09 PM, Navneet Kumar Singh wrote:
> Thank You Sir!
> I just removed the ligand part from the system.
> Used Peptides+Water--Used pdb2gmx to create .gro file
> converted the ligand.pdb in to .gro using command *gmx editconf -f unk.pdb
> -o unk.gro*
> combined the peptides+water.gro and ligand.gro to form ----complex.gro
> updated the number of atoms.
> Took a single UNK_fix.mol2 file and converted it to unk.itp file using the
> method described in the protein-ligand complex tutorial at mdtutorials.com
> Then updated the unk.itp and unk.prm file information in topol.top file.
> Performed the energy minimization and everything went fine.
> Sir is this right approach ?

Generally if you succeed in minimizing the structure, it's a good 
indication that everything is OK.



Justin A. Lemkul, Ph.D.
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