[gmx-users] (no subject)

[Jorden Cabal]

I think the answer is not so straightforward. It depends upon a lot of
things, but I would say that the parameters derived using QM is better. If
you do not have any other options you can still use PRODRG server but even
in that case, I find many people using the docked (or bound) conformation
of the Ligand molecule to generate the initial parameters, which in my view
should not be done. One should generate the parameters using the molecule
in its minimum energy conformation instead of bound conformation.
I would also suggest you to look at the RED server. Please follow this link
https://upjv.q4md-forcefieldtools.org/RED/

Thank you

On Mon, Aug 19, 2019 at 3:00 PM Priyanka Singh <prinebula23 at gmail.com>
wrote:

> Hii
> I am new to simulations. I want to ask is it ok to use ligand topology
> build using PRODRG server if using amber force field for RNA-ligand
> simulation. what precautions one should take ends of the RNA molecule.
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