[gmx-users] Dynamics of the salt-bridges

James Starlight jmsstarlight at gmail.com
Sun Feb 3 07:01:54 CET 2013


thanks again for suggestions.

I'm not quite sure how I can use tpbconv -zeroq. For example I want to
reduce charges of all amino acids except Asp Glu and His ( to monitor
s.b dynamics between that groups only).

As I understood -zeroq working with the groups defined in the index
file so I should just  select all residues that I need in that file,
shouldnt it  ? Also doest it possible to select pairs of residues
placed in the sequence on the distant sites ? (e.g by selecting only
pairs within some range of n1 and n2+k where k>n1+10)


2013/2/2 Justin Lemkul <jalemkul at vt.edu>:
> 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
> --
> ========================================
> 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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