Daniel and Ross,
I was just asking if there is a way to find atoms from periodic images
within a given cutoff of an atom in the primary cell, something like the
"pbwithin" macro of VMD.
I carefully decided the box dimensions to avoid such effects. The protein
C-teminus was pinned down with coordinate restraints to eliminate diffusion
and use a smaller box, as I am only interested in the dynamics o the
N-terminus. It appears that I have set the Z-dimension a few Angstroms
shorter than it should be. In my opinion, that periodic contact resulted
from an unnatural stretch on the folded part of the protein and a
concurrent unfolding of the flexible N-terminus that was driven by its high
positive charge and perhaps the ions (I use a NaCl concentration of 0.15
mM) that bridge the positive N-term with the negative C-term on the
periodic cell. Since the simulation has progressed too much, I would prefer
to give a flick to the N-term so that it goes away from that position and
let the molecule adopt a "more natural" conformation. And of course I will
not include that part of the trajectory in my analysis.
Is it possible to apply a force along the Z-axis with NMR-based restraints?
I have found an older post in the list which says that modification to the
code must be made.
thanks,
Thomas
On 28 January 2013 03:07, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Thomas,
>
>
> This is not possible in AMBER and even if it was I do not believe that it
> will do what you actually think it will do. Any restraint to an image can
> be recast as an internal restraint, since you have periodic boundaries and
> cannot be anything other than this. Placing a minimum distance restraint
> between the C terminal of your protein and the N terminal of an image is
> exactly the same as placing the same restraint between the two ends of the
> central protein with the distance and sign of the force constant just
> adjusted for the imaging. In effect all you will actually do is squash the
> two ends of your protein together compacting it which is what you
> definitely don't want to do. Ultimately you need to make the size of your
> solute box larger to avoid such periodic artifacts.
>
> All the best
> Ross
>
> On 1/27/13 10:22 AM, "Thomas Evangelidis" <tevang3.gmail.com> wrote:
>
> >Dear AMBER users,
> >
> >I would like to know if distance restraints between the protein in the
> >primary cell and one of its periodic images are allowed. The C-terminal
> >loop of my protein interacts at some point of the simulation with the
> >N-terminus of the protein in a periodic cell, and stays there for a long
> >time. To avoid that I would like to apply a force that moves away the
> >C-terminal loop whenever it reaching a cutoff distance from the periodic
> >image. Is this possible in AMBER?
> >
> >
> >thanks,
> >Thomas
> >
> >
> >--
> >
> >======================================================================
> >
> >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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> >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 Mon Jan 28 2013 - 03:00:02 PST
