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

Justin Lemkul jalemkul at vt.edu
Thu Jan 3 12:31:56 CET 2013

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.


> 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


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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