[gmx-users] PDB file that can be read in Gromacs

Phuong Chau pchau at smith.edu
Thu Mar 14 20:25:49 CET 2019

Hello everyone,

I want to generate gromacs topology of a substance (a single chemical)
which has a pdb file generated by RDKIT from SMILES representation of that
substance (MolToPDBFile). However, when I input the pdb file generated by
RDKit, it showed the error of "Residue 'UNL' not found in residue topology

The general idea is:
Input: Name of a substance (single chemical)
Output: pdb file of the substance (does not have to be generated by RDKit)
and the topology file of its susbtance that is generated by Gromacs.

Could anyone tell me any possible solution to solve this problem?

I am new to GROMACS.

Thank you so much for your help.
Phuong Chau
Smith College '20
Engineering and Data Science Major

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