[gmx-users] Requesting for Help on Hybrid CG-AA MD Simulations

[Maestre, Mitcheell]

M.szz mm sz

ms <devicerandom at gmail.com> schrieb:


On 7/8/14 12:35 PM, Yip Yew Mun wrote:
> Hi all,
>
> I wish to run a MD simulation with the protein in CG and the small organic ligand in AA. Has anyone attempted this before? If so, can guide me on how to generate the right topologies for such simulations?
>
> Thanks, any help would be greatly appreciated. =)
>

Hi,

In our group we run hybrid CG-AA simulations where we *also* leave some
of the protein in AA, to ensure a more accurate ligand/protein
interaction. You can find a few papers here:
http://digitallibrary.sissa.it/bitstream/handle/1963/1745/48_05.pdf?sequence=2
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047332#pone-0047332-g003
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0064675#pone-0064675-g007

In general, generating the topologies etc. for such a simulation very
much depends on the specific CG-AA method/setup you are using.

I hope it helps,
Massimo

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