Hi,
On Mon, Dec 30, 2013 at 4:04 AM, anu chandra <anu80125.gmail.com> wrote:
> wondering how the outtraj command understating that the parameters in data
> file is of eigenvectors ?. It can be of any form like RMSD values, distance
> etc.
>
Yes, the data can be anything. When reading in raw data, cpptraj doesn't
try to determine what the data is - it just reads it. So in the example I
gave before I was assuming you have a data file containing projections
along the first two principal components that looks something like:
#P1 P2
20.77 8.82
18.85 9.01
...
Note also that cpptraj can read data from xmgrace files (with extension
.agr) as well.
-Dan
>
> Many thanks once again
>
> Regards
> Anu
>
>
> On Thu, Dec 26, 2013 at 8:05 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > 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
> > > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> >
> >
> > --
> > -------------------------
> > 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)
> > _______________________________________________
> > 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
>
--
-------------------------
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 Tue Dec 31 2013 - 08:30:02 PST
