[gmx-users] Generation of the Distance Restraints

[Justin A. Lemkul]

James Starlight wrote:
> Francesca,
> 
> Yes I suppose this is good aproach for the generation of position 
> restricktions on the desired atoms. But I want to restrain the distance 
> between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of 
> two different residues).
> 

How many restraints do you need to create?  If they are this simple, you can 
write them yourself using a text editor in conjunction with manual section 
4.3.4.  Using genrestr is only really helpful when you require a network of 
distance restraints between the atoms of a given group.  If there are only a few 
to create, it's actually more work to use make_ndx and genrestr than it is to 
fire up your favorite text editor.

> Also I want to restrain some dihedral angles in the desired rotameric forms.
> 

See manual section 4.3.3 and 
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints.

> In literature I've found that peple have dome the same things in Gromacs 
> but I could not find detailed algorithm of such methodology :(
> 

All relevant equations are provided in the manual, and examples are provided 
either there or on the Gromacs site.  If you need further information, ask a 
specific question related to what you can't find or don't understand.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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