On 1/3/13 5:15 AM, Kavyashree M wrote:
Dear users,
I would like to add that in case of ARG or LYS, the sidechain
nitrogen atoms (NE,NZ,NH1,NH2) are present in the output.
The problem s only with GLU and ASP residues.
I use 4.5.3 version
I only took a quick look through the code, but it seems that what g_saltbr is
doing is labeling its output files based on the first atom in a given charge
group. The charge group, not the individual atoms per se, are what dictate the
search criteria. You haven't said which force field you're using, but I will
assume it's one of the Gromos ones, wherein the C[GD] atom is the first atom in
the COO- charge group.
-Justin
Thank you
kavya
On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M <hmkv...@gmail.com> wrote:
Dear users,
I used g_saltbr to calculate the salt-bridge interactions using:
g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep
It gave the output for each atom-atom interaction within
the given cut-off.
When I checked the atom type that corresponds to the atom
number output in each file, side chain oxygen atoms of ASP
and GLU was not present in any of the file. And most of the
atoms that corresponds to the ASP and GLU were CB, CG or
CD.
Kindly someone clarify why is this so.
Thank you
Kavya
--
========================================
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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