[gmx-users] residue UNK not found- how to generate force field parameters?

Jacob Nowatzke jn681 at humboldt.edu
Tue May 10 02:21:40 CEST 2016

I want to take a fatty acid amide, oleamide, and toss it around in a
bilayer, eventually.

Right now, I am fine with solvating oleamide in water, just to get to that
point would be wonderful.

The title captures my issue- I don't know how to generate proper force
field parameters and implement them in GROMACS- I can find no definitive
walk-through on the issue, and it seems some older GROMACS web pages are no
longer available.

May I ask the community for any leads on a simplified overview of how to
generate proper topology for a compound such as oleamide, to implement said
compound into GROMACS MD simulations?

I am sure my lack of expertise shows- I'm aware I am out of my league,
however if I can walk through tutorials, there's not much reason I can't
branch out to use my own choice of ligands/non-proteins after learning how
to generate these needed definitions.

Any help is greatly appreciated. My end goal for oleamide is simply a MD
simulation with annealing from 310K to ~275K, over a varying time frame.
Right now, of course, I'm concerned with getting past residue 'UNK'.

Thank you!

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