[gmx-users] Result analysis of protein water

[Deep kumar]

Thanks Smith,



On Fri, Sep 8, 2017 at 7:38 PM, Smith, Micholas D. <smithmd at ornl.gov> wrote:

> First: Welcome to the wonderful world of MD.
>
> Second, 10ns for a 164 residue protein is nowhere near enough simulation
> time. If you are looking for just small modifications, you could do an
> alignment of the backbones of the proteins in each trajectory and compare
> all frames to all-frames using the rmsd (you'd end up with a matrix of rmsd
> values comparing trajectory 1 to trajectory 2).
>

I am looking to perform conformational (such as if due to mutation protein
unfolds) and free energy change after the mutation. Please let me know what
kind of analysis should be done for such an aim. And, please share how many
ns MD is apt for 164 residues or more.

>
> Other things to consider are: salt-bridges, hydrogen-bond networks, and
> secondary-structure measurements (STRIDE or DSSP).
>

Could you please share more details on how these analysis can be performed?


Thanks much!


>
> Good Luck.
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Deep
> kumar <deepak.choubey86 at gmail.com>
> Sent: Friday, September 08, 2017 12:30 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se; gmx-users at gromacs.org
> Subject: Re: [gmx-users] Result analysis of protein water
>
> Hello All,
>
> I have performed MD on a protein water for 10ns, protein with total 164
> residues in two chains. I have got the result graphs of radius of gyration
> and rmsd for both wild and mutant. Wanted to attach the graphs but could
> not due to bytes limit. There is one residue mutation (M -> T) in the
> protein. I am new to MD analysis. Could you please let me know how to know
> if the mutation is causing any conformational change. I can look at the
> trajectories obtained of wild and mutant type, but to make accurate
> analysis I would need more information. Also, please do share with me how
> can i do more analysis to see the effect of mutations. Please let me know
> if I need to provide more information.
>
> Thanks & Regards.
> --
> 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.
>
> --
> 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.
>