[gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins

[Justin Lemkul]

On 9/21/12 2:33 PM, James Starlight wrote:
> Dear Gromacs Users!
>
> In some recent publications about protein dynamics investigation I've
> found reference about new gromos force field (56A7) where some fix in
> case of dihedral terms have been included.
>
> During my simulation performed with the 56A6 ff I've noticed that in
> some cases short alpha helices fragments were unfolded during 50-100ns
> of simulation. In particular that was in cases of simulation of
> membrane receptors. In some of that proteins I've observed unfolding
> of the part of the alpha helices which were placed in the water layer
> ( the rest of the alpha helices embedded in the membrane layer was
> very stable during all simulation time ). So I wounder to know if that
> events were the artifacts of the 56A6 force field or there are some
> biological-significance of such dynamics seen in the water layer.
> Is it possible to obtain new 56A7 ff and integrate it into Gromacs (
> I'm using version 4.54). ?
>

54A7 force field files can be obtained from ATB:

http://compbio.biosci.uq.edu.au/atb/

> Will the systems (topologies) made for 56A6 ff compatible with the
> 56A7 ff ( In particular I'm using Berger's lipids) or should I create
> my protein-in-membrane system again ?
>

If you're using a different force field, you have to recreate the topologies.

-Justin

-- 
========================================

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

========================================