[gmx-users] Salt bridge observation

[Justin Lemkul]

On 4/4/13 12:27 AM, Kavyashree M wrote:
> Sir,
>
> That is true, previously you had explained regarding this.
>
> Calculation using g_saltbr
> 1. For g_saltbr I included the following residues -
>      ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated
>      which contained only these residues. sb was calculated using -
>
>     g_saltbr -f traj.xtc  -s md.tpr  -b 4000 -e 4000 -t 0.4 -sep
>
> 2. Files that were generated were filtered and only those having
>      sb between ASP, GLU and ARG LYS were retained.
>
> 3. Further, out of these sbs, those which had the following atoms
>      CG  ASP, CD  GLU, NE  ARG, NH1 ARG, NH2 ARG, NZ  LYS
>      were retained.
>
> Calculation using g_hbond -
> It was done using the index file mentioned in my previous post using
>
> g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm
> -hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000
>
> So essentially the final results in both are composed of sbs formed
> between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr
> while charged atoms in case of g_hbond.
>
> The comparison showed that all sbs from g_hbond were present
> in the output from g_saltbr. But g_saltbr had some additional sbs
> off-course between the same charged groups. But only the distance
> was greater than 4 Ang for ex-
> distance between NH2 ARG and OD2 ASP is 4.32Ang
> Since it considers charged group CG of ASP instead of OD2 ASP
> distance between NH2 ARG and CG ASP is 5.54 Ang
>

So g_saltbr is doing something weird, though I don't see how it is possible to 
be honest.  It's up to you to filter the information by what you believe to be 
useful.  An NH2-CG salt bridge likely doesn't make any sense at all, anyway.

-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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