There are many papers on MD simulations of proteins with carbon nanotubes using AMBER force field. I was wondering if anybody can provide parameters (frcmod or lib files) for carbon nanotubes in AMBER format?
Dear Neha,
carbon nanotubes come in many different sizes, chiralities and with different functional groups. So you will have to generate the files for each kind of CNT accordingly.
A good first try might be the generalized AMBER force field (GAFF). Parameters can be generated via a tool called acpype from the respective atom coordinates.
See here: http://pubs.rsc.org/en/content/articlehtml/2018/fd/c8fd00011e
The GAFF parameters were optimized for small organical compounds. So if you want to simulate quantities that probably deviate, for example bending rigidities, you might have to adapt the parameters according to existing literature or refine them yourself.
Best regards,
Martin
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