[gmx-users] g_lie query

Anirban Ghosh reach.anirban.ghosh at gmail.com
Tue Dec 28 18:58:27 CET 2010


Thanks a lot Justin for the reply !!!

While calculating the Elj and Eqq values should we consider the short-ranged
LJ (LJ-SR) or LJ-14, the two components that are present in the .edr file?
And for Coulomb also?
Which one should we consider?

Thanks again.

Anirban


On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Anirban Ghosh wrote:
>
>> Thanks a lot Justin for the reply.
>> Yes I am going through all the relevant literature on LIE.
>> Actually the lie.xvg file contains the same value of -25.4 for all the
>> frames. So I am getting a straight line plot. Why is this happening? Am I
>> missing out something?
>>
>>
> If the interactions of your ligand and its receptor are stable, then there
> may be no change in the energetics.  I don't know anything about your
> system, so I can't say anything beyond that.
>
> -Justin
>
>  Thanks a lot again.
>>
>> Anirban
>>
>>
>> On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Anirban Ghosh wrote:
>>
>>        Thanks a lot Justin for the reply.
>>        So I ran a simulation with my ligand in water for 1 ns and using
>>        g_energy I calculated the LG-14 and Coulomb-14 values from the
>>        .edr file. I supplied the average of these two values as my Elj
>>        and Eqq to g_lie and I got the DGbind as -25.4. Is this the
>>        correct way to do this?
>>
>>
>>    Again I would ask you to not rely entirely upon my advice for this.
>>     I have only examined the LIE method sparingly.  My best answer is,
>>    "probably," but do read the literature on the method to be sure.
>>
>>
>>        And why am I getting only a single value of DGbind for all the
>>        frames captured in the .edr file?
>>
>>
>>    The lie.xvg file contains the LIE values as a function of time.
>>     What's printed to the screen is the average value and standard
>>    deviation.
>>
>>    -Justin
>>
>>        Thanks a lot.
>>
>>        Anirban
>>
>>
>>        On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul
>>        <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>        <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>>           Anirban Ghosh wrote:
>>
>>               Thanks Justin for the reply.
>>               I have through the threads about g_lie, but cannot
>> understand
>>               how to get the values for Elj and Eqq for a particular
>>        ligand.
>>               Like in my case for a system consisting of a beta2AR
>>        protein +
>>               dopamine (ligand) + POPC + water, what should be the
>>        values for
>>               Elj and Eqq?
>>
>>
>>           To obtain these (from my limited understanding), you would
>>        have to
>>           run a simulation of your ligand in water, decomposing the
>>        nonbonded
>>           energies between the ligand and solvent into LJ and Coulombic
>>           components.  Those are your values.
>>
>>           I should also note that simply going through the archive to
>>        inform
>>           yourself about the LIE method is insufficient.  The original
>>           literature, and several subsequent papers (one at least
>>        within the
>>           last year, IIRC), describes the accuracy of the method and
>>        what it
>>           needs to be properly run.
>>
>>           -Justin
>>
>>               Thanks a lot.
>>
>>               Anirban
>>               On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul
>>               <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>        <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>               <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>        <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
>>
>>
>>
>>                  Anirban Ghosh wrote:
>>
>>                      Hi ALL,
>>
>>                      I have run a protein + ligand (dopamine)
>>        simulation. Now
>>               I want
>>                      to calculate the free energy of binding using
>>        g_lie. But
>>               g_lie
>>                      asks for two values: Elj and Eqq. How or from
>>        where can I get
>>                      these values for my ligand? Also, do I need to run a
>>               simulation
>>                      with only the ligand? And, is there any other way
>>        (like
>>               MMGBSA
>>                      in Amber) to calculate the free energy for my
>>        simulation? Any
>>                      suggestion is welcome.
>>                      Thanks a lot in advance.
>>
>>
>>                  Go to the literature and understand what information is
>>               needed for
>>                  such a simulation, and then look into the list
>>        archives and
>>               you'll
>>                  find dozens of threads about using g_lie.
>>
>>                  -Justin
>>
>>
>>                      Regards,
>>
>>                      Anirban
>>
>>
>>                  --     ========================================
>>
>>                  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> <http://vt.edu>
>>        <http://vt.edu> | (540)
>>
>>               231-9080
>>
>>                  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>                  ========================================
>>                  --     gmx-users mailing list    gmx-users at gromacs.org
>>        <mailto:gmx-users at gromacs.org>
>>               <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org
>> >>
>>                  <mailto:gmx-users at gromacs.org
>>        <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
>>        <mailto:gmx-users at gromacs.org>>>
>>
>>
>>                  http://lists.gromacs.org/mailman/listinfo/gmx-users
>>                  Please search the archive at
>>        http://www.gromacs.org/search before
>>                  posting!
>>                  Please don't post (un)subscribe requests to the list.
>>        Use the www
>>                  interface or send it to gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>
>>               <mailto:gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>>
>>                  <mailto:gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>
>>               <mailto:gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>>>.
>>
>>                  Can't post? Read
>>        http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>           --     ========================================
>>
>>           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> <http://vt.edu> | (540)
>>        231-9080
>>           http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>           ========================================
>>           --     gmx-users mailing list    gmx-users at gromacs.org
>>        <mailto:gmx-users at gromacs.org>
>>           <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>
>>           <mailto:gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>>.
>>           Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>    --     ========================================
>>
>>    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
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
>>    --     gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at 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-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
> --
> ========================================
>
> 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101228/095a13bb/attachment.html>


More information about the gromacs.org_gmx-users mailing list