[gmx-users] PROTEIN FOLDING

[Neha Gupta]

Ok..Thank you..

I'll extend my simulation upto 50 ns.

Thanks,
Neha

On Tue, Dec 19, 2017 at 12:44 PM, Nikhil Maroli <scinikhil at gmail.com> wrote:

> After MD simulation of protein-ligand complex for 5ns, can we view protein
> folding?
>
> mostly, NO
>
> Search what time range 'protein folding' is happening.
>
> How to do it?
>
> I want to ascertain if there is any conformation change in protein where
> the ligand binds. Is it possible?
>
>
> You might want to do PCA, RMSD and DSSP
>
> We observe hydrogen bonds through molecular docking. Hence, I want to make
> observation through MD simulation which is not obtained through docking.
>
>
> gmx hbond
>
> Can someone help me regarding this?
>
>
> i really wondering what is possible in 5 ns simulation time, you may
> try to extend it up to 100 ns or atleast a 50 ns.
>
> Thank you very much in advance.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>