[gmx-users] Salt bridge analysis tool

[Justin Lemkul]

On 3/14/13 10:14 PM, albielyons wrote:
> Hi,
>
> I am trying to analyse my trajectory for specific salt bridges and the only
> program I can find is g_saltbr with the -sep command, which gives back all
> atom pairs that come within the set cutoff at any point in simulation time,
> whether they are charged and H-bond partners or not and regardless of
> whether they are together long enough or just glancing past each other.
>
> This means that I am getting 80 000+ "salt bridges" in my protein, which is
> obviously incorrect. I cannot find any other program to analyse salt
> bridges, does anyone know if there is a better one? Or if there is a way to
> make g_saltbr's results more specific and managable.
>

tpbconv -zeroq can be used to zero out charges on groups that are not of 
interest, thereby reducing the number of charge pairs that can be detected.

g_dist can also be used to measure distances between specific groups that you 
are interested in.

Either approach requires creation of index groups that specify groups of interest.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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