[gmx-users] freeze area around ative site

[Anton Feenstra]

Joanne Hanna wrote:

> Hi
> 
> What I am wanting to do is simulate my solated protein but only allowing the atoms within a certain radius of the ligand to be mobile, I assume I would use the freeze groups option to freeze everything outside this radius, however does anyone know of a method to calculate the radius and which atoms are outside?
> any advice would be much appreciated.

Use any basic modeling program, or even Rasmol could do it, I think. 
(Otherwise, an awk or perl script could process your coordinates fine 
enough.)


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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