tleap can be used to prepare systems, probably the real question here is
whether you have complete coordinates for the system that you want to
simulate, or if any model building is needed. tleap is not intended for
model building and has very limited abilities. Papers discussed in this
review from a few years ago may give you an idea of what others have done
to set up their simulations
https://www.sciencedirect.com/science/article/pii/S0959440X1730132X
On Mon, Apr 26, 2021 at 2:17 PM Shirin Jamshidi <shirinjamshidi.gmail.com>
wrote:
> Dear Amber Developers & Users,
>
> I am going to simulate the 50S subunit of ribosome including RNA and
> protein using the AMBER 16 program. I just was wondering whether the only
> approach is generating the primary system (prmtop & inpcrd) using CharmmGUI
> webserver or it is possible to prepare the system in tleap as well.
>
> Best,
> Shirin
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Received on Mon Apr 26 2021 - 12:00:02 PDT
