On 2/1/13 3:22 PM, James Starlight wrote:
Dear Gromacs users!
I have trajectory from which I want to investigate dynamics of all
possible salt bridges (E.g distance between adjacent + and - charged
residues) of my protein during the simulation
As I understood ussage of g_saltbr -t -sep could be suitable for such
thing but I'm not sure in validness of -t for definition of the native
salt bridges ( e.g with the default settings g_saltbr produced huge
number of all possible combinations of the polar contacts within my
protein ). Is there any others gromacs tols for such investigation?
Not really. If you're looking for any possible combinations of charged
residues, g_saltbr is the only way to go. The default value of -t basically
means everything is always considered, which you may not want. A more
physically relevant truncation distance is probably warranted, but it's been a
long time since I've played with it. You can always make subset trajectories
(with matching .tpr files from tpbconv) to analyze smaller chunks of residues
and ignore things you may not care about, like ions.
-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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