Dear Daniel,
Thanks for your prompt reply. I have a quick question here. I just
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.
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
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> > 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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>
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Received on Mon Dec 30 2013 - 03:30:02 PST
