[gmx-users] Salt bridge observation
hmkvsri at gmail.com
Thu Apr 4 10:34:08 CEST 2013
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.
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:
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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