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

[Justin Lemkul]

On 5/9/16 8:21 PM, Jacob Nowatzke wrote:
> 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'.
>

Oleamide should be very straightforward to put together based on available 
parameters (you haven't said which force field you want to use, but they should 
all support it).  Models in additive force fields are typically built by piecing 
together building blocks, here an amide (e.g. Asn/Gln side chain) and an alkyl 
chain that has an unsaturation.  Pretty straightforward.  You'll need to consult 
both theoretical and experimental literature to find/generate suitable target 
data for validation; this is why there are few, if any, full tutorials on 
parametrization.  It's very difficult to find a robust example that has lots of 
useful data for it.

Once you have some initial parameters, abandon these generic "UNK" labels and 
name your residue something sensible.  The incorporate it into an .rtp entry and 
follow 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

It's rather straightforward to add a residue; what's more difficult is obviously 
coming up with the parameters, but that's not a GROMACS issue per se.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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