Ragothaman Yennamalli wrote:
Message: 1
Date: Tue, 05 Jul 2011 19:14:04 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] free energy calculations
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4e139abc.1030...@vt.edu <mailto:4e139abc.1030...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Ragothaman Yennamalli wrote:
> Hi,
> I want to run free energy calculations on a particular protein-ligand
> complex. I do not have much knowledge on this so I have some
questions,
> hopefully someone might give me clear answers.
> I am following the tutorial given in this link:
>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html
>
> My questions are as follows:
> 1. I am assuming that I do not need the "protein without the ligand"
> form for free energy calculations. Am I right?
>
Free energy calculations can be done on a number of systems. The
tutorial is
just one simple example.
Thanks for the mail. So, I technically do not need both the un-complexed
and complexed form of the protein with the ligand.
This is discussed in the tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html
> 2. To use g_bar, I need to run the protein-ligand complex with
> a) first with lambda ranging from 0.5 to 1 for vdw coupling and
> b) followed by lambda ranging from 0.5 to 1 for coulombic
coupling
> Adding these would give the deltaG I am looking for. Am I right?
>
No. The range for lambda should be 0 to 1. Using 0.5 to 1 gives
only part of
the free energy for the transformation, and not necessarily half.
Apologies, I should have mentioned as from 0 to 1. So, the first step is
to do vdw coupling followed by coulombic coupling. Right?
No, the opposite. You do not want to remove vdW terms from charged species.
This topic is addressed in the tutorial.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/02_topology.html
-Justin
> 3. Are there any papers that use g_bar function in gromacs to
calculate
> free energy?
>
The g_bar tool is relatively new to Gromacs, so maybe not. The BAR
method
itself has been around for decades though, so its applications have been
demonstrated in the literature many times.
Thanks for pointing this.
Raghu
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/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
