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

Justin Lemkul jalemkul at vt.edu
Thu Mar 14 20:27:31 CET 2019

On 3/14/19 3:21 PM, Phuong Chau wrote:
> 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
> database".
> 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?

pdb2gmx isn't magic :)




Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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