GROMACS modification: Yes/No
Here post your question ’
I have 10 drug molecules from FDA (not in any databases) for which I want to perform MD Simulations. Somehow not able to generate the topology file for the drugs (ligands) due to their unsatisfied valances.
Can you suggest or guide me to generate a simulation without an STR file for these unknown molecules?
There are several online and offline tools to generate topology for ligands. You can try with the following servers
You also can refer Gromacs tutorial for protein-ligand complex for further understanding
You can’t generate a topology without having a complete structure, including all H atoms present. If you have unsatisfied valences, you need to complete the molecule. No server or program will work with chemically incomplete species.