[AMBER] Modeling 2D material with a bio-molecule/protein

From: Kashyap, Jatin <jk435.njit.edu>
Date: Sat, 10 Jul 2021 01:56:47 -0400

Dear AMBER Community,

I came across a paper https://pubs.acs.org/doi/10.1021/acsnano.0c09595
about modelling DNA interaction with a layered materials i.e. Single-Layer
Ti3C2 MXene . Authors had given brief information about using CHARMM GUI
for modelling all interaction between the atoms but I am not able to
replicate it through CHARMM GUI. Can anybody please guide what will be the
best approach to model such a system using AMBER. Or if there is any
tutorial that can be helpful. I want to replace DNA with protein.

Thank you.

Jatin Kashyap
PhD Candidate
Mechanical and Industrial Engineering Dept.
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
(Phone) 201-889-5783 <(201)%20889-5783> (MEC 333H)
(Email) jk435.njit.edu
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Received on Fri Jul 09 2021 - 23:00:02 PDT
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