Re: [AMBER] capturing free energy landscape

From: anu chandra <anu80125.gmail.com>
Date: Thu, 26 Dec 2013 17:29:03 +0530

Dear all,

Thanks to all the valuable replies. Finally, I could able to generate the
free energy landscape considering PC1 and PC2 as reaction coordinates. I
have a quick question here. How can I go back and capture the protein
conformers seen at the local minima regions in free energy landscape (
blue-regions in the attached figure) ?

Figure showing the energy landscape is attached here for your reference.



Thanks in advance

Regards
Anu


On Fri, Dec 20, 2013 at 7:05 PM, Thomas Evangelidis <tevang3.gmail.com>wrote:

> load your prmtop file in VMD and do:
>
> [atomselect top all] writepsf system.psf
>
> That will a dummy .psf file just for the analysis you want.
>
>
>
>
> On 20 December 2013 10:55, anu chandra <anu80125.gmail.com> wrote:
>
> > Dear Thomas Evangelidis,
> >
> > As you said, I have looked at CPPTRAJ/PTRAJ in AmbeTools12 for an option
> to
> > convert .prmtop file to a .psf file. Unfortunately, I couldn't able to
> find
> > any action command in AmberTools12 for converting amber topology file to
> a
> > psf file. Is there any other way I can do this conversion?
> >
> > Waiting you valuable reply
> >
> > Thanks in advance
> >
> > Regards,
> > Anu
> >
> >
> > On Wed, Dec 11, 2013 at 4:39 PM, anu chandra <anu80125.gmail.com> wrote:
> >
> > > Hi,
> > >
> > > Thanks to all for the valuable suggestions. I will carefully look in to
> > > your replies.
> > >
> > > Thanks once again.
> > >
> > > Regards
> > > Anu
> > >
> > >
> > > On Wed, Dec 11, 2013 at 2:56 AM, Adrian Roitberg <roitberg.ufl.edu>
> > wrote:
> > >
> > >> BTW: careful with PCAs...
> > >>
> > >> First, make sure that the PCAs you choose represent a substantial
> amount
> > >> of the variance. Too many papers show 1 or 2 PCAS and the sum of them
> is
> > >> only 20% of the variance. Granted, it is the top 20%, but even then,
> it
> > >> is a small part of the story.
> > >>
> > >> Second, PCAS are notoriously hard to converge. Do this: take your 75
> ns
> > >> MD, split in into 2 halves. Redo PCA for each half separately and see
> if
> > >> the first PCA vector for one half is similar to the first PCA vector
> for
> > >> the second one. If not, then your PCA vecotr for the free energy is
> very
> > >> arbitrary and does not tell you too much about your system.
> > >>
> > >> Adrian
> > >>
> > >> On 12/10/13 3:59 PM, Thomas Evangelidis wrote:
> > >> > Carma does what Jason described automatically, namely you can plot
> the
> > >> Free
> > >> > Energy along two or three Principal Components. All you need is to
> > >> convert
> > >> > your .prmtop/.nc to .psf/.dcd with cpptraj from AmberTools. Check it
> > >> out:
> > >> >
> > >> > http://utopia.duth.gr/~glykos/Carma.html
> > >> >
> > >> > HTH,
> > >> > Thomas
> > >> >
> > >> >
> > >> >
> > >> > On 10 December 2013 22:45, Jason Swails <jason.swails.gmail.com>
> > wrote:
> > >> >
> > >> >> On Tue, Dec 10, 2013 at 5:23 AM, anu chandra <anu80125.gmail.com>
> > >> wrote:
> > >> >>
> > >> >>> Dear Amber users,
> > >> >>>
> > >> >>>
> > >> >>> I am working with all-atom MD simulations of protein-ligand
> system.
> > I
> > >> >> have
> > >> >>> carried out PCA analysis after 75ns of simulation. By looking at
> the
> > >> >>> collective motions along the first principle component, I could
> able
> > >> to
> > >> >> see
> > >> >>> that the protein is visiting two different conformations.Now, I am
> > >> >> looking
> > >> >>> for a method to capture the free energy landscape of these
> > >> conformational
> > >> >>> changes. If I am right, usual methodologies like meta-dynamics.
> AMD
> > >> etc.
> > >> >>> are usually used to overcome the high energy barrier during the
> > >> >>> conformational changes. Since I could capture the conformational
> > >> changes
> > >> >> in
> > >> >>> my protein during the classical MD itself, it seems like the
> energy
> > >> >> barrier
> > >> >>> is too low between these two different conformations. How can I
> > >> capture
> > >> >>> free energy change during these conformational changes? Which
> method
> > >> will
> > >> >>> be helpful for me to do this calculation?
> > >> >>>
> > >> >> If you have sufficient sampling without using any type of biasing
> > >> >> potential, you can just calculate free energies directly from the
> > >> >> simulation.
> > >> >>
> > >> >> This is typically done using a histogram along whatever reaction
> > >> coordinate
> > >> >> you choose to define and taking the negative log of the histogram
> > >> >> population (divided by the population of the most populated bin if
> > you
> > >> want
> > >> >> to set the minimum energy to 0). Multiplied by -kT, of course...
> > >> >>
> > >> >> Good luck,
> > >> >> Jason
> > >> >>
> > >> >> --
> > >> >> Jason M. Swails
> > >> >> BioMaPS,
> > >> >> Rutgers University
> > >> >> Postdoctoral Researcher
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
> > >> >> AMBER.ambermd.org
> > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>
> > >> >
> > >> >
> > >>
> > >> --
> > >> Dr. Adrian E. Roitberg
> > >>
> > >> Colonel Allan R. and Margaret G. Crow Term Professor.
> > >> Quantum Theory Project, Department of Chemistry
> > >> University of Florida
> > >> roitberg.ufl.edu
> > >> 352-392-6972
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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DeltG_landscape.png
(image/png attachment: DeltG_landscape.png)

Received on Thu Dec 26 2013 - 04:00:02 PST
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