[gmx-users] setting constraints to incomplete protein structures

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 30 00:37:17 CEST 2008

wk yeo wrote:
> Hello, all,
> It is quite common to encounter protein structures in PDB which consist of only the catalytic domain (versus the structure of the entire protein). One such example is: http://www.pdb.org/pdb/explore.do?structureId=1H1W 
> My questions:
> 1) Is it a good idea to use such catalytic domain structures for MD simulation? Or should I only use complete protein structures for MD?

That depends entirely upon what you are interested in simulating.

> 2) Is there a way to constraint the atoms using Gromacs during MD at the points where the catalytic domain is 'chopped' from the rest of the protein?

What you're looking for is known as a "restraint" within Gromacs.  Read the 
manual about position restraints and/or distance restraints.

> 2) If I want to use Gromacs to conduct a MD of 0.1ps at 300K, do I need to constraint any atoms at the 'edges' during the MD run?

What kind of "edges?"  Those that are adjacent to the missing segments?  If 
that's what you mean, see distance *restraints* or position *restraints*.


> Thank you.
> Regards,
> wk yeo
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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