[gmx-users] FW: Myristic Acid Simulations

[Justin Lemkul]

On 5/7/13 6:40 AM, Natalie Stephenson wrote:
>
> Hi,
>
> I know there have been many threads talking about parameterization of novel
> molecules for simulations within gromacs, but I just wanted to know if anyone
> had done any parameterization of myristic acid, as I intend to begin
> simulations on a protein that is myristolated and figured I'd check here
> before embarking on what sounds like it will be a very long and confusing
> process for a parameterization-newbie.
>
> I found a paper in which they've used myristic acid within their simulations
> (Ariel Alvarez et al., 2012, J.Biophys.
> http://www.hindawi.com/journals/jbp/2012/642745/) however they've only listed
> the topology coordinates of this molecule. Is it possible to create a .rtp
> from this topology? Would this require parameterization based on the force
> field I am using? If so where would I find information on the bond angles and
> dihedrals for this?
>

The nice part about Gromos96 parameter sets is that they're designed to be 
transferrable, i.e. you can build molecules piecewise from constituent 
functional groups.  Doing so usually gives you a reasonable topology.  You will 
have to adjust how the carboxylate is treated, since you don't have free 
myristic acid, but presumably some other covalent linkage to the protein.  I 
also wonder why those authors used 43A1; the lipid parameters in that set were 
rather poor, and alkanes were reparameterized in a later revision of Gromos96.

You can certainly create an .rtp entry from the listed topology.  See Chapter 5 
of the manual for details.  Bonded parameters are easy to introduce.  All that 
pdb2gmx requires is a [bonds] directive in the .rtp, and it figures out the 
angles and dihedrals based on the bonds.  Whether or not suitable bonded 
parameters can then be applied is something you will have to check, but for a 
simple acyl chain there should be no problem.  Again, 43A1 may be a poor choice, 
though, and you should consider a newer parameter set.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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