I am sorry I am not able to understand clearly what you are trying to model. Is the helix rotating ("rolling") or changing orientation relative to another helix ("pitching") as you mentioned in your earlier message?
Either way, the selection of a collective variable (or a reaction coordinate for a reaction generally speaking) has to be done with much thought and care. The details of system become fairly important, which are not available here.
Whatever you decide to use as a collective variable, make sure you allow plenty of time for conformational sampling in the umbrella sampling runs. If your protein system is medium to large, the change in helix conformation/orientation may not propagate quickly to other parts of the protein and you could see artifacts.
Good luck.
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 12/20/2018 10:24 PM, Akshay Prabhakant wrote:
Actually I am planning on finding the rotation of the axis of helix w.r.t.
to its initial state, since in my reaction, the axis of the helix
rotates(and also the helix itself) as we go from the reactant to the
product, so please can you suggest me something along these lines?
On Fri, Dec 21, 2018, 4:49 AM Pratul Agarwal <pratul.agarwal-lab.org><mailto:pratul.agarwal-lab.org> wrote:
This actually helps me! I didn't know about the NFE module, I am still
catching up on new features of AMBER18. Thank you Dr. Botello-Smith, I will
definitely look into it.
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 12/20/2018 6:11 PM, Wesley Michael Botello-Smith wrote:
As a clarification, nmropt was pretty much the only option for AMBER17 and
below (as Dr. Agarwal mentioned in a previous post).
As of AMBER18, you can now use the NFE module instead. See chapter 21.6.2
of the AMBER18 manual for details on how to use the NFE module for this, or
check out chapter 26 for details on doing this under the previous nmropt
method.
Hope this helps!
-Dr. Wesley Botello-Smith
On Thu, Dec 20, 2018 at 12:26 PM Pratul Agarwal <pratul.agarwal-lab.org<mailto:pratul.agarwal-lab.org>
<mailto:pratul.agarwal-lab.org><mailto:pratul.agarwal-lab.org>
wrote:
You will have to define your own collective variable based on what you are
trying to accomplish. The other messages in thread gave you some good
pointers about helix axis definition and using center of mass of atoms to
define the angle between two helices.
Practically speaking, you will have to use "nmropt" keyword if you want to
define angle between center-of-mass of groups of atoms and apply restraints
for umbrella sampling.
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 12/20/2018 12:13 PM, Akshay Prabhakant wrote:
I have a collection of atoms which forms a helical structure. I need to
find the vector corresponding to the axis of this helix, since I will be
using that as a collective variable in an umbrella sampling simulation. Can
someone please suggest me a way around?
A follow up question: How can i get angle between two vectors in amber as a
collective variable?
Thanks in advance.
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Received on Thu Dec 20 2018 - 22:00:02 PST
