[gmx-users] Dynamics of the salt-bridges

[James Starlight]

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.


James

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