[gmx-users] coordination number per residue
jalemkul at vt.edu
Sun Feb 24 19:27:44 CET 2013
On 2/24/13 12:53 PM, benrezkallah djamila wrote:
> Hello everybody,
> I am working on a system consisting of protein-ions in water box. I need
> to calculate the coordination number per residue for my protein, I have
> searched the gmx mailing list, and, I have not find the solution. please,
> can you help me with this, is anybody has a programm to look at the
> coordination number per residue?
I'm surprised there's nothing useful in the archive; there are hundreds of posts
related to coordination number. Even a simple Google search turns up a number
of useful results within the first few links.
There is no automated way to break down coordination number per residue; that's
your job to supply whatever tool you want to use (probably g_rdf) with a
suitable reference group. Luckily, creating such an index group is easy and
iterative calls to g_rdf (or whatever else) are easily scripted.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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