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

RAHUL SURESH drrahulsuresh at gmail.com
Thu Mar 14 21:03:01 CET 2019


First request, try to go through gromacs documentation and tutorials. You
will get the clue.

Topology of any nonprotein should be generated by a third party software or
scripts depending on the forcefield. Have a detailed look into the
tutorials. That will definitely help you.

Thank you

On Fri 15 Mar, 2019, 12:56 AM Phuong Chau, <pchau at smith.edu> 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?
> 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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