shiva birgani wrote:
Message: 1
Date: Tue, 31 May 2011 06:56:16 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] flexiblity
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4de4c950.70...@vt.edu <mailto:4de4c950.70...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
shiva birgani wrote:
> Dear all
> I have simulated two different proteins (A and B). I need to compare
> their flexibility. RMSF help to examine their flexibilty
individually,
> but I want to campare them with each other.
> Do anybody know a solution to this? Would you please help me in
this regard?
>
Is it not just a matter of comparing the RMSF between the two proteins?
-Justin
--
========================================
Dear Justin
Yes I want to compare them, but I am not sure that RMSF is appropriate
test to comparison, because two proteins are completely different in
their amino acid contents and numbers.
RMSF is the correct metric for measuring the flexibility of your proteins. How
you then interpret the data in light of what's known about your system and the
goals of your study is up to you. All part of good experimental design.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
