[gmx-users] Re : Simulation for prediction of binding between a peptide and protein

[Mark Abraham]

> Hi,
>
> I want to know how can I predict where a designed peptide will bind to 
> my protein target or not using simulation ... Can anybody guide me ??

I don't think anybody has the computational resources to answer this 
question with unguided MD. Docking programs are probably the way to get 
a guide about what binding modes might be reasonable, but I don't know 
what software might be fit for the purpose.

Mark