On 3/14/13 10:14 PM, albielyons wrote:
Hi,
I am trying to analyse my trajectory for specific salt bridges and the only
program I can find is g_saltbr with the -sep command, which gives back all
atom pairs that come within the set cutoff at any point in simulation time,
whether they are charged and H-bond partners or not and regardless of
whether they are together long enough or just glancing past each other.
This means that I am getting 80 000+ "salt bridges" in my protein, which is
obviously incorrect. I cannot find any other program to analyse salt
bridges, does anyone know if there is a better one? Or if there is a way to
make g_saltbr's results more specific and managable.
tpbconv -zeroq can be used to zero out charges on groups that are not of
interest, thereby reducing the number of charge pairs that can be detected.
g_dist can also be used to measure distances between specific groups that you
are interested in.
Either approach requires creation of index groups that specify groups of
interest.
-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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