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
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