[gmx-users] g_lie query
Justin A. Lemkul
jalemkul at vt.edu
Tue Dec 28 19:23:32 CET 2010
Anirban Ghosh wrote:
> Thanks Justin.
> Yes I did use PME during the simulations. But still when I process the
> .edr file with g_energy, it gives both the options...LJ-1-4 and LJ(SR).
> So if I am not wrong, I should be using the LJ(SR) value as the Elj in
> the LIE calculation. Right?
>
I'll have to assume that you're using a simple cutoff for LJ interactions, in
which case, yes, I think that would be the case. But if you used PME, you can't
properly determine an Eqq value, as I understand it.
-Justin
> Thanks again.
>
> Anirban
>
>
> On Tue, Dec 28, 2010 at 11:45 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Anirban Ghosh wrote:
>
> 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
>
>
> 1-4 interactions are intramolecular, thus should not be relevant to
> the LIE calculation.
>
>
> the .edr file? And for Coulomb also?
> Which one should we consider?
>
>
> Did you use PME? If so, you can't break down the Coulombic terms
> entirely.
>
> -Justin
>
>
> Thanks again.
>
> Anirban
>
>
>
> On Tue, Dec 28, 2010 at 11:03 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 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>
> <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:
>
> 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>>
> <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 <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:
>
> 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>>>
> <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 <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>
> <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 <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> <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>>>
> <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
> <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>
> <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
> <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>>>
> <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
> <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>
> <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
> <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> <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>>>
> <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
> <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>>
> <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
> <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/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> <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/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>>
> <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/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> <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
========================================
More information about the gromacs.org_gmx-users
mailing list