Creating a .gro file from a .itp file

User discussions
1

GROMACS version:5.1.5
GROMACS modification: No
Here post your question : Is it possible to create a .gro file from an .itp file?

Hi users,
I want to create a .gro file for urea. I am using amber99sb-ildn forcefield which has urea.itp in it but to include urea as a co-solvent to my protein I need to have urea.gro file.

Please suggest me how to generate a gro file for urea.

Thanks,

Sweta.

2

Hi Sweta,

There are a bunch of options to obtain such a structure

  • Openbabel and the urea SMILES can help you here. This works for all types of ligands.

  • Lots of X-ray structures have urea in them. Downloading the .pdb and deleting everything but the urea ATOM/HETATM entries will give you a urea pdb. If you have urea in a .pdb file, you can also use this for gromacs, you can convert .pdb to .gro with gmx editconf as well as gmx trjconv (use .pdb for both structure and trajectory in the latter case). Note that gromacs can also just go ahead with .pdb files.