[gmx-users] Query of RMSD results

[Sainitin Donakonda]

Dear Micholas,

Thanks for reply, I used g_rms routine

As per my knowledge i understand that if protein  ligand complex has high
RMSD over protein only RMSD then it means that ligand has some influence on
protein backbone.

But in my case i saw low RMSD value for protein-ligand in comparision to
protein only . Now i am confused what to interpret for this result. Can you
please suggest some insights?

Thanks,
Sainitin

On Wed, Oct 29, 2014 at 2:07 PM, Smith, Micholas D. <smithmd at ornl.gov>
wrote:

> Which routine did you use for your RMSD calculation: g_rms or g_rmsdist?
>
> If your reference structure was the first frame of your trajectory (the
> default, I believe), than what your rmsd measure is telling you is that the
> protein-ligand complex "average" deviation from it's initial conformation
> is less than the protein on its own (slightly). See chapter 8 of the manual
> for details on how the calculation is performed. Also look at Maiorov &
> Crippen, Proteins
> 22, 273 (1995)
>
>
> ===================
> 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 Sainitin
> Donakonda <saigro16 at gmail.com>
> Sent: Wednesday, October 29, 2014 8:54 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Query of RMSD results
>
> Hello,
>
> I performed 20ns MD simulation on 2 types systems
>
> 1) Protein only
> 2) Protein-ligand 1 complex
>
> Then did RMSD analysis on both systems i observed that following RMSD mean
> as follows
>
> Protein only : 0.45 nm
> Protein-ligand 1 complex: 0.40
>
> Now i am confused how to interpret this result as protein-ligand complex
> RMSD is lower than apo form of protein.
>
> Can any body please explain how to explain these results
>
> Thanks,
> Sainitin
> --
> 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.
>