[gmx-users] Salt bridge observation

[Kavyashree M]

Sir,
Why I mentioned NH2 CG saltbridge because the g_saltbr
gives the charge group and does not mention the OD2 of ASP
but mentions only CG. Otherwise it does not make any sense.

Thanks
Regards
Kavya


On Thu, Apr 4, 2013 at 1:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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