[gmx-developers] Making personal plugin

[Jonathan Khao]

Anton Feenstra a écrit :
> Jonathan Khao wrote:
>> Anton Feenstra a écrit :
>> Thank you for your responses. Effectively , I haven't been clear on 
>> what we intend to do.  My system is a Protein Detergent Complex, and 
>> our goal is to know how atoms behave are along the faces of an alpha 
>> helix. So we wanted to make a tool that read a Trr file, and 
>> converted the coordinates  as a function of :
>>        - the position along the axis of the protein ( fitted to the Z 
>> axis )
>>        - the distance from the axis
>>        - and an angle
>> So correct if I'm wrong, as you suggested, the use of gromacs's 
>> functions to read the "trr" trajectory is not worth it, a custom made 
>> tool should therefore be more appropriate ? If so are there any 
>> instructions on how to "decrypt" the "trr"  files ?
>
> There is somewhere a template tool (template.c IIRC) that is basically 
> an empty program that just reads coordinates from your trajectory. 
> That should get you started.
>
> Also, there is at least one tool that is specific for the analysis of 
> helices, IIRC it can do axis fitting.
>
>> I've also been working on an other project for some time. I wanted to 
>> get properties of some molecules (detergents) which are in the 
>> vicinity of my alpha helix. The properties that I want to get are 
>> avaliable using the gromacs tools. But where I need help, is in the 
>> selection of the molecules in the "vicinity".
>>
>> I've done verry heavy programming scripts which computes the 
>> distances of each molecules ( degergents ) with the g_mindist , then 
>> i read each of the "xvg" files , got the intervals where it was under 
>> the cutoff value, made sub trajectories, concatenated them and then 
>> applyed the gromacs tools. I suppose there are easy shortcuts to 
>> follow , especially by avoiding the time spending printing and 
>> reading parts.
>> So could you help me by  telling me how i could apply a filter on the 
>> tools ? It would be verry usefull, and would at last help me to dive 
>> in the gromacs source code.
>
> I'd suggest modifying g_mindist to suit your needs. It's been a while 
> since I been through that code, so I'm not sure how easy it is to read 
> it.
>
> Another tool you might want to use for this, is g_hbond. Although it 
> is developed for H-bonds, with the proper setting of angle- and 
> distance cutoffs, and donor and acceptor atom/types, you should be 
> able to get more general info on solvent/detergent vicinity. Plus, 
> g_hbond is reasonably optimized for large-scale pairwise distance 
> calculations (it uses neighboursearching).
>
>
Thanks verry much !  I'm on it ;)

-- 
Ph.D. Jonathan KHAO
LISM-IBSM-CNRS
31 Chemin Joseph Aiguier
13402 Marseille Cedex 20
France
jkhao at ibsm.cnrs-mrs.fr
tel : 0616738391