[gmx-users] Re: distance restraint

Justin Lemkul jalemkul at vt.edu
Fri Sep 28 21:39:55 CEST 2012

On 9/28/12 3:34 PM, pauladelgado wrote:
> <http://gromacs.5086.n6.nabble.com/file/n5001418/Screenshot-2.png>
> This is the distance of one pair of atoms that i restraint.
> I apologize if i did't mention why i am using distance restraint, i am
> working with a protein obtained using homology modelling, the next step
> after i get the protein structure is doing molecular docking, the problem is
> that i need to refine the structure and i found in literature that the
> protein goes through a conformational change where it forms a bundle of 4
> alfa helix (hydrofobic interactions) before it interacts with its ligand, so
> besides of making the refinment of the structure i need  to obtain that
> bundle in order to do molecular docking. The reason for doing the refinement
> in vacuo is that when you minimize a struture to avoid steric clashes i
> always make them in vacuo with other software, the problem is that i need to
> form the bundle and the software i usually used doesn't handle position
> restraint.  My intention never was to bother you,   I am very thankful for
> your time to answer my questions.

The distance shown is constant at roughly 8 nm.  Your topology specifies that 
the desired restraints (though there are multiple, so are we to assume that all 
of the distances are similar?) are in the ballpark of 0.5 nm.  The use of 
distance restraints is not to severely modify a structure.  Instead of doing 
this, the algorithm will fail, as you are seeing, resulting in very large 
energies.  I don't know if this is a viable route for the refinement you seek - 
if very large structural changes are expected, then extensive MD simulation will 
be required.  Conformational changes can occur spontaneously or can be induced 
with steered MD (pull code), though care needs to be taken with the latter 
approach, as undesired structural changes can certainly occur if done incorrectly.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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