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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>
--
======================================================================
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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Received on Fri Dec 20 2013 - 06:00:04 PST
