Hi,
You could potentially do this with the 'outtraj' command in cpptraj using
the 'maxmin' keyword. For example, if your raw PC projection data is in a
file with two columns, you would first read in that data, then read in the
corresponding trajectory, then use 'outtraj' commands to capture frames
corresponding to certain PC ranges, e.g.:
readdata pc.dat
trajin mytraj.nc
outtraj Min1.nc maxmin pc.dat:1 min 25 max 40 maxmin pc.dat:2 min 15 max 20
Hope this helps,
-Dan
On Thu, Dec 26, 2013 at 4:59 AM, anu chandra <anu80125.gmail.com> wrote:
> 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
> > > >>
> > > >
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > 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/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
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>
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Dec 26 2013 - 07:00:03 PST
