[gmx-users] (no subject)

[Justin Lemkul]

On 8/19/19 2:00 AM, Priyanka Singh 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.
PRODRG is for GROMOS and produces very low-quality topologies. You 
cannot combine GROMOS topologies with AMBER (nor can you mix and match 
any force fields). Do everything with one force field. AMBER + GAFF is a 
much better option.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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