On 4/2/13 11:58 AM, Kavyashree M wrote:
Sir,
Thank you very much for your reply. I wanted to calculate
Salt bridge in the whole protein so i am not mentioning the
residues involved. The problem with g_saltbr was that if I
have to calculate the accessibility of these atoms it will be
a problem because it gives the charge groups but not exact
atoms.
This is the reason I thought of using g_hbond. But I wanted
clarification from experts in using this method.
So Is there any problem if I use g_hbond?
Does this really give you any useful information? You'll get an output file
with putative contacts derived from an arbitrary cutoff for any possible
positive-negative pair defined in the index group. I think the g_dist approach
is far more useful and gives you exact insight into specific pairs. It takes a
bit more prep work, but looping the calculations is trivial to do to make them
efficient.
-Justin
Thank you
kavya
On Tue, Apr 2, 2013 at 9:03 PM, bipin singh <bipinel...@gmail.com> wrote:
You can use g_dist with specific atoms indices to calculate distances,
if you already have the information about atoms involved in salt
bridge interactions.
On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M <hmkv...@gmail.com> wrote:
Dear users,
Kindly clarify my doubt regarding salt bridge calculation.
Thank you
Regards
Kavya
On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M <hmkv...@gmail.com> wrote:
Dear users,
For calculating salt bridge in proteins I
am using g_hbond instead of g_saltbr.
In g_hbond I use contact and mention two
indices consisting of
group 1: ASP_GLU_&_OD1_OD2_OE1_OE2:
group 2: ARG_LYS_&_NZ_NE_NH1_NH2:
I use the command:
g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm
matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 50000
Is this approach correct?
Thank you
Kavya
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Thanks and Regards,
Bipin Singh
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========================================
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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