AMBER Archive (2009)

Subject: Re: [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent"

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jan 20 2009 - 08:33:55 CST

first let me say that what you want to do (folding/dimerization) is
very advanced and not really for a new user, or someone just doing the
tutorials. folding a peptide is far different from concurrent
folding/aggregation.
it is possible to add such a restraint in amber- though amber10 is
much easier than amber9.
likely you should add a distance restraint using nmropt=1 on the
center of mass of the 2 peptides (using the igr1 arrays), and include
a large flat region before any penalty is applied (in your case, r3 of
20.).
as I said, this is an advanced simulation, so if the above doesn't
make sense (check p178 of the amber9 manual for the distance restraint
details) then maybe it's best to do some more basic simulations first.
good luck!

if you still want to do it, probably want to restrain the centers of
mass of the peptides.
On Mon, Jan 19, 2009 at 4:03 AM, Jagadeesh, M.N., Ph.D.
<mnjaga_at_gmail.com> wrote:
> Dear AMBER users,
>
> I have a question on "distance restraint between center of mass of two
> peptides" (say 10 residue peptide with all Ala).
>
> I have been performing small peptide folding simulations with implicit
> solvent like the one explained in Ross Walker's (very nice)
> Tutorial-8<http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/>
> .
>
> Now, I want to do such folding simulation for two peptides (to check
> dimerization probability). As a new user I tried without any restrains and I
> could see that during heating phase itself, molecules start moving away from
> each other. So, I realize that I have to put some restrains so that they see
> each other.
>
> I came across a paper in "The journal of Chemical Physics 129, 195102 (2008)
> The Alzheimer beta-amyloid (Abeta(1-39)) dimer in an implicit
> solvent<http://www.ncbi.nlm.nih.gov/pubmed/19026087>"
> where they have done some nice trick to keep two molecules together in a
> sphere of 20Angstroms, similar to what I want to do. From the paper *"We
> confine the molecules within a sphere of given radius through adding an
> attracting harmonic force. The harmonic constant is K(r-r0)**2/2 when the
> distance between the center of mass of two AB molecules exceeded 20 A, and
> zero for shorter distance."*
>
> Basically this is like tying two molecules with a elastic band of 20 A. How
> to translate this in to amber input files?
>
> Further search reveal that I have to use nmropt=1 and put force constants
> and distance restraints in a seperate DISANG file, here I am lost... and it
> may be obvious for some of you how to put info together and this is where I
> need your help in getting exact clues about creating DISANG file to set up
> my "virtual elastic band of 20A".
>
> Thank you.
> Jagadeesh
> PS: I'm using AMBER9
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