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

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