RNA and aminoacid ligand force field

User discussions
1

GROMACS version: 2021.4-Ubuntu-2021.4-2
GROMACS modification: No

I am working on producing a simulation of and RNA molecule binding its ligand, which is a lysine molecule. I have doubts when it comes to modelling the ligand to introduce. For the RNA I am using the Amber94sb force field, downloaded from GROMACS. My question is wether I can use that same force field to generate the topology of my ligand, as it is an aminoacid with no modifications. In that case, it would be just generating the topology as I did with the RNA molecule and including it into the main topol file? Or should I create the initial topology with both the lysine and the RNA in the same .pdb file?

Thanks :)

2

Hi there,
You may use https://github.com/alanwilter/acpype for ligand topologies while using parent Amber Force Fields.

1 Like
3

Hi Pallav,

Thank you for your answer! I am beggining to learn all of this on my own and there are still some things that scape me. I have used acpype, but I thing that something must have gone wrong, because when I do the energy minizamion step, I get a really high potential energy (10^7). I had run a simulation of the RNA molecule before without the ligand and that em step had a “normal” PE, according to the tutorial (around -10^6). Is it something expected or should I revise my work?

4

You can plot the PE from the edr file and check.