[gmx-users] Re: g_saltbr not include side chains of GLU and ASP??

[Kavyashree M]

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

Thank you
kavya

On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M <hmkvsri at 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
>