AMBER Archive (2009)

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

From: Jagadeesh, M.N., Ph.D. (mnjaga_at_gmail.com)
Date: Mon Jan 19 2009 - 03:03:39 CST

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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