On Thu, Sep 21, 2023, Abhilasha Thakur wrote:
If anyone is using the AMBER OL3 force field kindly send it to me. I am
working on RNA str prediction.
I think the official source of OL3 parameters is here:
https://fch.upol.cz/ff_ol/
This will cite the correct references. OL3 is based on earlier Amber force
field work, but was developed outside of the Amber project.
To actually see the parameters, download AmberTools:
https://ambermd.org/GetAmber.php. The force field files will be in the
"dat/leap" folder.
If all you want is the force field parameters themselves, you don't need to
compile anything. If you want to actually use the force field to evaluate
RNA structures, you will need to build AmberTools as well. (Easier for most
people is to download the pre-compiled conda package.)
Please note that force fields like OL3 are designed for simulations with
explicit solvent (water + ions). Fairly good results can also be obtained
using a generalized Born implicit solvent model. You should not expect to
get useful results with just the RNA coordinates alone.
...dave case
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