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

[Justin Lemkul]

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 :)

http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database

-Justin

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Justin A. Lemkul, Ph.D.
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