[gmx-users] FW: Myristic Acid Simulations

Natalie Stephenson natalie.stephenson at manchester.ac.uk
Tue May 7 12:40:08 CEST 2013


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?

Any advice on creating a .rtp file would be greatly appreciated!!


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