[gmx-users] Dynamics of the salt-bridges

Justin Lemkul jalemkul at vt.edu
Sat Feb 2 19:08:44 CET 2013

On 2/2/13 12:18 AM, James Starlight wrote:
> Justin,
> I suppose that the ussage of the sub-set of trajectories is suitable
> when you've already known possible salt-bridge pairs. But that time
> I'd like to obtain that information from my trajectory.
> E.g I have membrane-embedded protein which is the buddle of
> alpha-helixes. I want to examine dynamics of the salt-bridges between
> helixes first of all ( that interactions might serve as the
> conformation locks ).
> For such taks I've tried to use smaller -t distance with g_saltbr (e.g
> considering dynamics of the residues within 1nm assuming both broken
> and closed salt-bridges as well as taking into account that my protein
> is membrane-bound where helixes   are situated closely than in
> water-soluble proteins) but again that produced many wrong pairs.

Defining "wrong" is a context-dependent assessment that can only be made after 
the fact.  You can also probably reduce the number of putative salt bridges by 
using tpbconv -zeroq on various groups; there is a threshold within the g_saltbr 
program for deciding (based on magnitude of charge) if a group is a putative 
salt bridge participant.

Beyond that, accept the fact that g_saltbr is extremely unwieldy and 
post-process accordingly.



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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