RAHUL SURESH drrahulsuresh at gmail.com
Tue Dec 19 08:23:03 CET 2017

On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <nehaphysics17 at gmail.com> wrote:

> Hi gromacs users,
> After MD simulation of protein-ligand complex for 5ns, can we view protein
> folding?

You can use various supporting tools from R language to debug your
trajectory but most third party software support NAMD and charmm format.
You can use VMD to convert the trajectory to dcd and use R language based
packages to read your trajectory

> How to do it?
> I want to ascertain if there is any conformation change in protein where
> the ligand binds. Is it possible?
> We observe hydrogen bonds through molecular docking. Hence, I want to make
> observation through MD simulation which is not obtained through docking.
> Can someone help me regarding this?
> Thank you very much in advance.
> Thanks,
> Neha
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*Rahul Suresh*
*Research Scholar*
*Bharathiar University*

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